The Islam influences have arrived in Ende between 16th till 17th century. While the Portuquese arrived in Malaka in 1511. The Dutch East India Company was established in 1602 especially in Ende of Flores island.

After their arrival in the area, the Portuguese made Solor (an eastern island off the mainland Flores) the centre of their trade. Repeated attacks on Solor by the Javanese seafaring traders suggest that the island had already been used as a trading port by the Javanese (especially for the sandalwood derived from Timor). Nagarakertagama mentioned that Solot (Solor-Flores) belonged to Majapahit. The small island called Pulau Ende in the Bay of Ende seems to have served the same purpose for the Javanese.

In the 1561, the first Bishop in Malaka sent three missionaries to Solor, where after an attack by the Javanese Muslims, then constructed a fortress. Also, on Pulau Ende, the Portuquese constructed a fortress there. The two fortresses are the main scenes of the struggle among the Portuguese, Muslims and, later on, the Dutch.

A tale of struggle between the Christians and the Muslims on Pulau Ende was told in a legend about a beautiful woman, Rendo, the daughter of the commander of the fortress. That tale is usually referred to as Rendo Rate Rua, or Rendo of the Two Tombs. The story is as follows

Rendo was the daughter of a Portuguese commander of the fortress and a Numba woman. She had a long hair which was repa rhima rua (seven yards), siku rhima rua (seven elbows), pangga rhima rua (seven hands), fate rhima rua (seven cubits) long. And her throat was so white that one could see the water going down through it

When her father was away from the fortress, a troop of Javanese pirates attacked the fortress. Rendo's lover Jebe Jawa, a Javanese working in the fortress, was killed at that time.

The leader of the pirates, Ndoke Rua, was going to take Rendo away; but she and her slave, Tonjo, managed to escape from him. They ran to a place called 'Eko Reko bringing a golden tray with them

The two women threatened the pirates by making papaya leaves look like a cannon. This trick, however, did not work for long. Then Rendo and Tonjo were about to jump into the sea, when they found a fisherman. They asked him a favour and borrowed his boat.

When Ndoke Rua, with his pirates, arrived at Eko Reko, Rendo and Tonjo were already in the middle of the sea. Ndoke Rua, finding no boats available there, prayed for rain and wind. There came big waves and their boat sank. Rendo and Tonjo died. Rendo father moved to Royo Hayon

Rendo has two tombs: one on the island; and another in Numba, which now serves as a boundary between two ritual domains called Tana Rhorho and Tana Dea. The slave, Tonjo, turned into a flower, which is now called by the name of Tonjo.

Van Suchtelen collects a shorter version of the same story. The interesting difference is that the bad guy, Ndoke Rua, is, in this version, a priest working in the fortress. The struggle between the Portuguese and the Muslims (not only Javanese, but also native people who had been converted to Islam) continued on the island of Flores.

After some years of peace, in 1605, the Portuguese on Pulau Ende were driven out by the natives to a village on the mainland Flores, called Numba. At the beginning of the 17th century, there happened an interesting episode in the history of Flores, which tells us the relation between a Makassarese princedom and some native headmen on Flores. In 1602, a native headman, called Ama Kira (according to Rouffaer; the original Portuguese rendering of the name is Amequira) raised the war, and Ama Kira asked for the help of a Makasarese prince, who sent a fleet under the command of a man called Dom Joao (apparently once a Christian). The fleet under Dom Joao attacked the fortress on Pulau Ende, and was defeated. Dom Joao, after the defeat, returned to Makassar, and the prince of Makassar sent rice to Solor and concluded a peace with the Portuguese

The fortress on Pulau Ende was burned down. Since this time until its recovery in 1613 Pulau Ende was abandoned by the Christians

1613 is a significant year in the history of eastern Indonesia. A Dutch fleet under the command of Apollonius Scotte (or Scot) sailed through the islands. Before arriving at Kupang, Scotte went to Solor and attacked the fortress there and took it from the Portuguese. The Portuguese, or more precisely, the `black Portuguese' fled to Larantuka, which, from that time, became the centre of the black Portuguese. The Dutch attacked Larantuka also, but failed to take it. Adrian van der Velden, Scotte's deputy commander, went to Ende, and found the ruin of the fortress there

In the decades between 1610 and 1640, the Portuguese in Larantuka and the Dutch on Solor played a kind of see-saw game, which, in the long run, turned in favour of the Dutch.

The Portuguese in Larantuka, in 1616, managed to defeat the Dutch on Solor and regained the fortress, only to lose it again in two years. In 1618, the Dutch made an assault on Larantuka, and failed. In 1625 and 1629, the Portuguese attacked the fortress, and in the latter battle, the fortress became the possession of the Portuguese. But the Portuguese occupation of Solor did not last for ten years. In 1636, attacked by the Dutch, the Portuguese had to abandon the fortress again, and this time, forever.

The fortress on Pulau Ende had been destroyed earlier in 1620 (the exact date is unknown). Unlike Solor, which remained significant in the Dutch Company/Colonial Rule context, Pulau Ende ceased to play any important role. The city of Ende, where the rajadom of Ende may already have formed, replaced Pulau Ende as a focus point in central Flores. Around this time, the Portuguese influence over the area waned.

Even though the formal transference of Flores from the Portuguese to the Dutch took place as late as 1851 and 1859 (eastern Flores), the Portuguese began to lose their control over this part after 1657, when the Dutch East India Company established Fort Concordia in Kupang and the Dutch began to set a strong hold on the area.

Through the 17th and 18th centuries, there are occasional references to the relations concluded between the Dutch East India Company and some Endenese headmen.

Baraai, a coastal Endenese village about 6 km west of the city of Ende, recognized its subordination to the Company and received a ``posthouder'' in 1691. The posthouder, though, seems to have stayed there only for a short time

The Company selected Ende as a rajadom. In 1756, the rajadom of Ende is said to have exported its cinnamon to the Company. This fact suggests that even though there were many equally strong headmen in central Flores, Ende became conspicuous among them by this time.

The Dutch East India Company's involvement in eastern Indonesia ended in 1799 when the Company's charter expired. Then came a new era of the Dutch Colonial rule in Indonesia.

This era can be divided, in central Flores, into two periods, 1907 marking the transition between the two. During the earlier period, there was no serious intervention by the Dutch Government in Flores. This period can be further divided into two: (1) the period before 1890 and (2) that after 1890. In the former period, the Dutch colonial rule had virtually no hold over the region.

An incident, which reveals the not so simple relationship between the Endenese raja and the Dutch Government, happened in the year of 1890, the year which, according to one officer (de Vries), demarcates the period before 1907.

In June 1890, a Kupang-interned prisoner Bara Nuri, an Endenese headman, escaped and returned to Ende. The Dutch Colonial Government requested the raja of Ende to help the Government catch Bara Nuri. After repeated failures, mainly due to the Dutch government's reluctance to help cooperate with the raja, the raja finally managed to capture Bara Nuri.

On returning to Ende, Bara Nuri called for help and set himself up in a village, Manu Nggoo. The raja of Ende (Aru Busman) attacked the village, in vain.

On the 8th of January 1891, the warship Java appeared in Ipi bay of Ende. With this help and about 1,000 men gathered by the effort of the raja, the raja attacked the fortification of Bara Nuri, on the 10th of January, and failed again. In February, reinforcements came from Kupang: the cruiser van Speijck.

Seeing that Bara Nuri would not surrender despite the repeated attack of the raja and the Dutch force, the posthouder (Rozet) sent for a truce. After concluding the peace, Bara Nuri came out, only to be captured by the posthouder, an act of ``treachery'' on the posthouder's side. Some of the headmen told de Vries later in 1910 that the posthouder had said to Bara Nuri that Bara Nuri should come to Ende so that people could choose him as Raja.

In 1896, the raja, Pua Note, was formally appointed as raja of Ende by the Dutch Government.

When another war broke out between the raja of Ende and some other villages (Nanga Baa and Watu Sipi) in 1904, the Government quickly sent a ship, H.M. Mataram, to help the raja.

sources WIKIPEDIA