Abstract Nasuta-albomicans complex (NAC) of Drosophila is an artificial hybrid zone comprising of Drosophila nasuta nasuta, Drosophila nasuta albomicans and 16 Cytoraces, which are the evolutionary products of a long range hybridization experiment conducted in the laboratory environment. Occurrence of centric fission in the X3 chromosome of Cytorace 1 led to the derivation of Fissioncytorace-1. Molecular techniques have emerged as powerful and valuable tools for detection and exploitation of genetic polymorphism. In the present study, Cytorace 1 and Fissioncytorace-1 were subjected to Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR) analyses to determine the introgression of D. n. nasuta and D. n. albomicans genomes. It was found that Cytorace 1 and Fissioncytorace-1 exhibit similarities in RAPD and ISSR profiles although different combinations of genomic regions could have favoured Fissioncytorace-1, for better morphophenotypes and fitness, when compared to Cytorace 1, whi...