25 RFLP analysis of the mtDNA D-loop region in Hilsa shad (Tenualosa ilisha) population from Bangladesh ABU SHUFIAN ISHTIAQ AHMED, MD. SHAHIDUL ISLAM, MD. SHARIFUL AZAM, MD. MUKHLESUR RAHMAN KHAN AND MD. SAMSUL ALAM Department of Fisheries Biology and Genetics, Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh ABSTRACT The genetic structure of three populations Hilsa shad (Tenualosa ilisha), be- longing to three different ecological zones such as freshwater (Chandpur), brack- ish (Kuwakata) and marine (Cox’s Bazar) were studied by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of mito- chondrial DNA. Fifteen composite haplotypes, representing information from 7 restriction enzymes were generated for samples of 7 fish from each site. All populations have polymorphic haplotype and the haplotype diversity (h) of the three populations were 0.979, 0.979 and 0.918 for Chandpur, Kuwakata and Cox’s Bazar respectively. The intra-population nucleotide diversity was 36.75% in Chandpur and Kuwakata and 25.56% in Cox’s Bazar population. These in- dicate that the genetic variability of the present Hilsa shad population falls within the range of good condition and the genetic status of Hilsa shad does not appear to be affected, though the catch has decreased due to overexploitation and indiscriminate killing. Genetic distance between Chandpur and Kuwakata populations, Chandpur and Cox’s Bazar, Kuwakata and Cox’s Bazar were 0.0213, 0.1823 and 0.1610 respectively. UPGMA dendrogram shows that the Chandpur and Kuwakata populations are very close group and Cox’s Bazar population is a different group. Introduction Hilsa shad is an important diadromous clupeid fish widely distributed in the south and southeast Asia, especially in Bangladesh. It constitutes the largest single species fishery in Bangladesh, found in almost all the big river systems, estuaries and the Bay of Bengal, contributing at present 12.9% of the total catch that includes a biomass of 75060 metric tons from inland fisheries and 154654 metric tons from marine fisheries (DoF, 2002). However, the production of hilsa in Bangladesh seems to be declining, compared to the earlier estimates (Mia and Shafi, 1996). Until 1972, the hilsa fishery was extended up to the upstream of the Padma and Meghna Rivers. At present the fishery has severely declined in the upstream and has been mainly concentrated in the downstream rivers, estuaries, coastal areas and the sea (Rahman and Haldar, 1998). Low water Indian J. Fish., 51(1) : 25-31, Jan.-Mar., 2004