I know that some borders in the past were created based on the religion of the people living there, hence the split between Belgium and the Netherlands. Was this the same case?
The Soviet Union established the borders between these now states in 1924 and 1928 (Tajikistan went from an ASSR to SSR in this year). Uzbeks, Tajiks, and Kyrgyz all lived in this area with weird borders known as the Fergana Valley. It has very robust soil and is known for cotton growth. The Soviets based the divisions on ethnic lines based on the 1897 Russian census, the most recent one performed. The next census came in 1926, which helped in the delineation of the borders for the Tajik SSR. The Soviets attempted to give all three ethnic groups the part of the valley that was mostly inhabited by that group. An important example against this is the town of Osh which was Uzbek but became part of the Kyrgyz SSR.