Abstract: Yellow catfish (Pelteobagrus fulvidraco) is an important aquacultural fish species in China. Since hydrid breeding is an efficient method to improve aquaculture products, interspecific hybrid between Pelteobagrus fulvidraco and its close species Pelteobaggrus vachelli that grows faster than Pelteobagrus fulvidraco, has been massively produced. However, it is hard to distinguish Pelteobagrus fulvidraco from the interspecific hybrid by morphological features. Moreover, the interspecific hybrid could not being used as parents for the existence of sterile hybrids. Previously, we constructed a bacterial artificial chromosome (BAC) library from YY super-male yellow catfish and screened out a BAC clone containing the sex-linked marker, Pf62-Y. In this study, we identified a novel gene inad-like in Pelteobagrus fulvidraco after sequencing the BAC clone, and the exons of inad-like are the same in X and Y chromosomes. Moreover, we cloned partial intron sequences of inad-like in Pelteobaggrus vachelli based on the exon sequences of inad-like in Pelteobagrus fulvidraco. Interestingly, there is a small segment deletion in Pelteobaggrus vachelli in compa-rison with the corresponding sequence in Pelteobagrus fulvidraco. Based on the significant genetic difference between Pelteobagrus fulvidraco and Pelteobaggrus vachelli sequences, we designed one pair of primers, by which 1908 bp and 1178 bp were amplified in Pelteobagrus fulvidraco and Pelteobaggrus vachelli, respectively. Moreover, both 1908 bp and 1178 bp were amplified in the interspecific hybrid. Together, this new genetic marker develops a highly stable and efficient method for distinguishing Pelteobagrus fulvidraco and its interspecific hybrid.