History of Kota Kinabalu
Let's go back in time.
Since 15th century, the area of what is now Kota Kinabalu came under the influence of the Bruneian Empire. In the late 1800s, the British North Borneo Company (BNBC) began to establish colonial settlements throughout North Borneo. In 1882, BNBC founded a small settlement in the area known as Gaya Bay, which was already inhabited by the Bajau people. The first settlement was at Gaya Island. However, in 1897, the settlement was burned and destroyed by the indigenous Bajau-Suluk chief Mat Salleh.

Jesselton, circa 1911
After the destruction, BNBC decided to relocate the settlement to the more easily defended mainland at Gantian Bay (now Sepanggar Bay) in 1898. However, Gantian Bay was found to be unsuitable and in July 1899, Henry Walker, a Land Commissioner, identified a 30 acres (12 ha) site opposite Gaya Island as a replacement for Gantian Bay. The replacement settlement site was a fishing village called Api-Api. The site was chosen due to its proximity to the North Borneo Railway and its natural port that provided good anchorage, which was up to 24 feet deep.
By the end of 1899, construction had started on shoplots, a pier and government buildings.This new administrative centre was renamed Jesselton after Sir Charles Jessel, who was the then Vice-Chairman of BNBC. Eventually, Jesselton became a major trading post of North Borneo, dealing in rubber, rattan, honey, and wax. The North Borneo Railway was used to transport goods to the Jesselton harbour. The Malay and Bajau uprisings during those times were not uncommon, and BNBC worked to quell the long-standing threat of piracy in the region. Jesselton was partially razed by the British during their retreat from the advancing Japanese and suffered further devastation when the Allies bombed it in 1945. After the Japanese takeover of Borneo, it was again renamed Api. Several rebellions against the Japanese military administration took place in Api.
One major rebellion in the town occurred on 10 October 1943 by a group called Kinabalu Guerrillas in the Jesselton Revolt consisting of local inhabitants. Japanese forces quelled the rebellion after its leader, Albert Kwok, was arrested and executed in 1944. At the later stages of the war, what remained of the town was destroyed again by Allied bombings day and night for over six months as part of the Borneo Campaign in 1945, leaving only three buildings standing. The war in North Borneo ended with the official surrender of the Japanese 37th Army by Lieutenant General Baba Masao in Labuan on 10 September 1945.
After the war on the edge of bankruptcy, the British North Borneo Company returned to administer Jesselton but was unable to finance the huge costs of reconstruction. They gave control of North Borneo to the British Crown on 18 July 1946. The new colonial government elected to rebuild Jesselton as the capital of North Borneo instead of Sandakan, which had also been destroyed by the war. The Crown Colony administration designed a plan, later known as the "Colonial Office Reconstruction and Development Plan for North Borneo: 1948–1955", to rebuild North Borneo. This plan provided £6,051,939 for the rebuilding of infrastructure in North Borneo. When the Crown Colony of North Borneo together with Sarawak, Singapore and the Federation of Malaya formed the Federation of Malaysia in 1963, it became known as Sabah, and Jesselton remained its capital. On 22 December 1967, the State Legislative Assembly under Chief Minister Mustapha Harun passed a bill renaming Jesselton as Kota Kinabalu. The city was upgraded to city status on 2 February 2000.
Etymology

Kota Kinabalu is named after Mount Kinabalu, which is situated about 50 kilometres east-northeast of the city. Kinabalu is derived from the name Aki Nabalu meaning the "revered place of the dead." Aki means "ancestors" or "grandfather", and Nabalu is a name for the mountain in the Dusun language. There is also a source claiming that the term originated from Ki Nabalu, Ki meaning "have" or "exist", and Nabalu meaning "spirit of the dead".
The word kota comes from Malay word kota which in turn comes from the Sanskrit word कोट्ट (kota) which means fort, fortress, castle, fortified house, fortification, works, city, town, or place encircled by walls. It is also used formally in a few other Malaysian towns and cities, for example, Kota Bharu, Kota Tinggi, and Kota Kemuning. It can also be used informally to refer to any towns or cities. Hence, a direct translation of the name Kota Kinabalu into English would be "City of Kinabalu" or "Kinabalu City".
"Kina Balu from Pinokok Valley" – lithograph published in 1862.
Original names
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Besides Jesselton, there are also other older names for Kota Kinabalu. The most popular is Api-Api, or simply Api, which is a Malay word meaning 'Fire'.[4] Wendy Law Suart wrote in her book on North Borneo, The Lingering Eye, "there is in the Sabah State Museum a Dutch map of Borneo and the Celebes dated 1657 in which the settlement where Jesselton was to stand is clearly labelled Api Api. It may have some connection with the seaside tree with breathing roots that bears the same name". There are claims, however, that Kota Kinabalu was actually named after a nearby river called Sungai Api-Api. In Chinese, the city is still known as 'Api', which is the Hakka pronunciation for 亚庇 (Simplified Chinese; Traditional Chinese: 亞庇; Pinyin: yà bì).
Another suggested historical name is Deasoka, which roughly means "below the coconut tree" in the Bajau language. The Bajau locals purportedly used this name to refer to a village in the southern part of the city which was filled with coconut trees. Yet another name was Singgah Mata which literally means "transit eye", but can be loosely translated as "pleasing to the eye". It is a name said to have been given by fishermen from Gaya Island referring to the strip of land that is today's downtown Kota Kinabalu. Today, all these names have been immortalised as names of streets or buildings around the city. Some examples are Lintasan Deasoka, Api-Api Centre and Singgah Mata Street.