The word Qarauna derived from Mongolian word Khara meaning black. At first they were subjects to Great Khan and served as tamnas or tamachis in Afghanistan and modern Pakistan. Great Khan appointed their leaders from non-Chingisid generals such as Dayir and Mungudei. In 1238, they settled near India to face military forces of Delhi Sultanate. In 1250's their leader was Sali who was a general of tatar origin. Muslim lords arranged that 100,000 dinars be brought to Sali Noyan by the ghulcim and in return the commander would withdraw his troops from Multan. Mongols invaded India several times for booty and slaves.
Mongke Khan ordered Sali and his tamna soldiers to join Hulegu's army in 1253. In 1260, Jochid princes Kuli, Baval and Tutar died. Cursed Baval, the father of Nogai, was executed by the order of Hulegu Khan after taking permission from Berke who was the khan of Jochid Ulus/Golden Horde. Soon after that, Kuli and Tutar died suspiciously. Golden Horde soldiers, who served for Hulgeu, feared. They started to move to Kipchak steppes via Derbent and Egypt. Angered Hulegu punished many soldiers of Golden Horde for the defeat of Ain Jalut. Mongol general Baiju was executed as well. To the east, the flight of Jochid troops into Afghanistan in significant numbers led to the creation of the Negudari (Nikudari) Mongols or Qaraunas in 1262. Berke ordered general Neguder to raid eastern part of Ilkhanate. Sometimes, historians call Qara'unas as the Neguderis. This term was derived from the name of Negudar.
Although some scholars claim that this group owed allegiance to no khanate until it was largely brought under Chaghatayid control in the 1290s, it is known that they were incorporated into Chagatai Khanate during the reign of Alghu in 1262. As a result of wars between Mongol khanates, Qara'unas deserted Hulegu and captured Sali bahadur. While majority of Qara'unas was ruled by Chagatai princes, their another group in Khorasan formed the eastern border defensive for Abagha Khan. He appointed former Chagatai Khan Mubarak Shah their leader.
Duwa recalled his cousin Abdullah and appointed his son Qutlugh Khwaja a governor there in 1299. The descendants of Duwa had ruled Qara'unas since then. Oljeitu reasserted his ancestors' claim on Afghanistan and repelled Qara'unas in 1314. Another Chagatai prince Yasa'ur was given lands in Afghanistan by the latter Ilkhan. Thanks to his complaisance towards both Buyantu Ayurbawda of the Yuan and Oljeitu, Kebek reoccupied the territory peacefully. Esenbuqa, Eljigidey and Tarmashirin were all military governor of Qara'unas and became Chagatai Khans. This military group had attented all Mongol invasions of India since 1241.
Serving under the Khans, they gained confident from them. Because qaraunas were main force for the campaigns in Persia and India. Neguderis wintered around Ghazna and summered in Ghur and Garchistan. According to Marco Polo, they were mixed with Indians and Turks, because these soldiers were unable to reach Mongolia to find Mongol wives. After the death of Qazan Khan , Chagatai Khanate split into two parts until it was temporarily reunited under Tughlugh Timur (1347–1363). Chagatai mongol-turks fell under the control of semi-nomadic oboghs: the Arlat in the west, the Barlas in the centre, and the Jalayir in the north, and two non-tribal military groups, the Qaraunas and the Qa'uchin. In western part of the khanate was under the control of Qara'unas such as amir Qazaghan and his son ‘Abdullah. But Suldus and Barlas nobles revolted against their rule in 1359.
With the Mongol (Moghul) invasion in 1360, the Qarauna ascendancy failed. In 1362 Tamerlane (Temur, Timur) rejoined the Qaraunas under Qazaghan's grandson, Husayn. They freed Transaxonia from Mongols of Moghulistan, whom they considered Barbarians next year. But in 1365 the Moghuls invaded again. The Qarauna and Barlas forces were defeated.
Quickly after the Khan's fail, Timur and Husayn recovered. They co-ruled Maweranhar and installed puppet khan. Husayn decided to build himself a permanent capital and urban base on the site of Balkh in Afghanistan and Turkestan, ruined since the time of Chingis, but now to be developed as an anti Samarkand.When ambitious Temur finally revolted in 1370 at the head of his coalition, Husayn had little support left and he was easily defeated and killed.
During the reign of Temur (d.1405), Qara'unas formed a huge part of his army.
The Nikudari are (or were; Weiers notes that his informants were not aware of this term anymore) a population group of Afghanistan of Mongolic origin. While they don’t resemble Mongolians from their physical appearance as the Hazara people do, they are distinct from them in that the Hazara don’t exhibit any Mongolic linguistic peculiarities. The Nikudari, on the other hand, used to speak Moghol which is probably extinct now. Their tribal name hails from their former military leader, Negudar, who according to Morgan was a general of the Golden Horde, but according to the research of Weiers that Morgan fails to quote was a leader of rebels against Abaqa Khan.