The rule of Khwarezm shahs came to an end in 1220 when Mongol armies under Genghis Khan swept through the country.
After the conquest of China in 1218 Genghis Khan started plans for the invasion of Mawarannahr. In 1218-1219, a host of Mongols under the command of Ghengis Khan's general Jebe (the arrow) occupied the Kharnate of Kara-Khitan (now western china). In September 1219. Ghengis Khan came to Otrar, where he divided his army one under the command of his sons Ogadey and Chagatai to siege Otrar; another was given to Jochi and sent in the direction of Jend for the seizure of the towns along the banks of the Syr-Darya while he himself, with his son Tolui, headed for Bukhara.
The Khwarezm Empire which at that time controlled Mawarannahr (today's Uzbekistan) was not ready for the invasion of such a powerful enemy. The Mongols conquered and destroyed the oasis cities one after another. They first sacked Bukhara in February, Samarkand in March and by the autumn of 1220 Termez. When the mongols attacked Urgench (now Kunya-Urgench) in April 1221 the Khorezm Shah Muhammad beat a hastily retreat leaving his eldest son, a talented military commander Manguberdi to defend against the Mongolian invasion. It is said that Ghengis Khan oldest son Jochi engaged in negotiations with the defenders trying to get them to surrender so that as much of the city as possible was undamaged. This angered his older brother Chaghatai, and Genghis headed off this sibling fight by appointing Ögedei the commander of the besieging forces as Urgench fell. But with the removal of Jochi from command the Mongol forces proceeded to sack the city with great ferocity. As usual the artisans were sent back to Mongolia, young women and children were given to the Mongol soldiers as slaves, and most of the rest of the population was massacred. Then came the complete destruction of the city of Gurjang. Upon its surrender the Mongols broke the dams and flooded the city, then proceeded to execute the survivors. It is said by historians that up to 1 million people were killed during the sacking of the cities and towns of Khoresm oasis; making it at that time (and holding right up until the carnage of the 20th century) the bloodiest massacre in human history. According to legend Genghis Khan is famously quoted as saying "I am the punishment of God. If you had not committed great sins, God would not have sent punishment like me upon you".
The Mongol invasion of Central Asia which took place from 1219 to 1225 is one of the turning points in the history of the region and led to a wholesale change in the population of Mawarannahr. The conquest quickened the process of Turkification in the region because, although the armies of Genghis Khan were led by Mongols, they were made up mostly of Turkic tribes that had been incorporated into the Mongol armies as the tribes were encountered in the Mongols' southward sweep. As these armies settled in Mawarannahr, they intermixed with the local populations, increasingly making the original Iranian speaking inhabitants a minority. Another effect of the Mongol conquest was the large-scale damage the warriors inflicted on cities such as Bukhoro and on regions such as Khorazm. As the leading province of a wealthy state, Khorasm was treated especially severely. The irrigation networks in the region suffered extensive damage that was not repaired for several generations.
After the death of Genghis Khan in 1227 his vast empire split into several parts governed by his sons and grandsons. The northwest part of Uzbekistan joined the Golden Horde, possession of Genghis Khan’s firstborn Jochi, and the remaining part of the country known as the Chagatai Ulus passed to his brother Chaghatai (1227-1241). Despite the potential for serious fragmentation, Mongol law maintained an orderly succession for several more generations, and control of most of Mawarannahr stayed in the hands of direct descendants of Chaghatai, the second son of Genghis. This orderly succession allowed prosperity and internal peace to prevail in the Chaghatai lands, and the Mongol Empire as a whole remained strong and united for more than a century after the great Khan's passing.
Chaghatai's descendant Khan Kepek (1318-1326), a Jagataid, moved his capital to Maverannehr (now Uzbekistan and southern Kazakhstan). He built a palace near Nesef, which became the core of a large new city of Karshi (administrative centre of the present-day Kashkadarya vilayet). During the reign of his son Tarmashirin (1326-1334) who had converted to Islam, friction developed between two fractions of Mongol nobles; one faction advocated adopting Islam and settled lifestyles, and the other faction strongly adhering to nomadic traditions and pagan beliefs. This strife culminated in the country’s division into Maverannahr proper and Mogulistan. Further as a result of collisions between the two movements and feudal factions, in the late 1350s the Jagataids domain dissipated into more than a dozen petty states.
An interesting aspect is that Temudjin fathered so many offspring than recent genetic studies have found that in fact that of the current population of Central Asia that up to 1 in 10 are likely to be his descendants. This is a source of great pride and I understand that my own kids being Kipchaks are likely decedents as are many other Karakalpaks, Kazakhs and Uzbeks in both Karakalpakstan and in Uzbekistan as a whole.
Numerous studies by teams of biochemists, based on the Y-DNA of modern descendants of Genghis Khan, have indicated that Genghis Khan may have belonged to Haplogroup C-M217. The suggested 25 Marker "Genghis Khan" Y-DNA Profile is: