Abstract
Hatchery managers and maintaining genetic diversity and fitness population in endangered and threatened species in pond is a important and difficult thing to do. But is must to do for conservation biology. Fitness and structure population depends on effective breeding number (Ne) and population connectivity between each other. The second most important thing is gene flow and genetic drift. Ne is major role in the maintenance of genetic diversity as indicator for inbreeding depresion and genetic drift. We sampled 6 hatchery in Jakarta and Bekasi Indonesia region and used 12 polymorphic microsatellite loci to quantify population genetic structure. Result in this study are, each farm have different methode. The old farmers is bapakGusi and bapakHasan (+30 years). Ne in bapakHasan and bapakGusi hatcheryis 66,667 and F value is 0,00749 and loosing allele (P) is 0,26183. Compared with younger farmers bapakYahya (5 years) have Ne = 133,333, F = 0,00375 and P = 0,06855. Even though hatchery bapakHasan and bapakGusi have the same value Ne, F and P but the result in population structure they are different founder populations. Hatchery bapakHasan have unique structure and alleles composition compared with other hatchery.