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Despite the occurrence of a massive agricultural landscape change in Java, very few reliable studies evaluate its genetic consequence for impacted wildlife species. This study reported the genetic diversity of the Mandar besar (Porphyrio porphyrio) in the modified landscape of Java as a backdrop for such an evaluation. Aim of this study was to estimate genetic diversity and genetic structure of the species. I collected eighty-eight blood samples from five a-priory populations (Demak, Jombor, Kendal, Pagak, and Nawan) and genotyped them at ten selected microsatellite loci to estimate allelic richness (R) and expected heterozygosity (He), fixation index (FST) and genetic clusters (K). DNA was isolated using a commercial kit (Invitrogen) and amplified using touch-down polymerase-chain-reaction technique. Allele length was estimated using an automatic sequencer. Pre-analysis showed that all selected loci have null alleles frequency less than 0.2, successful amplification rate more than 80%, no significant linkage between loci and no deviation from HWE. Further analysis employing GDA and FSTAT showed that Demak population has richest genetic diversity in term of R, meanwhile Jombor was the poorest population. Analysis of population structure employing FSTAT and STRUCTURE showed that the population was likely structured into four subpopulations, as showed by FST (0.085; P<0.05) and K=4 (ln probability -1725.2+3.92). This study might reveal that genetic diversity and population structure of Mandar besar in Java were still in common level as compared to other aquatic bird species.Keywords :Swamphen, bird, richness, genetic, wetlands

GENETIC DIVERSITY AND POPULATION STRUCTURE OF MANDAR BESAR (Porphyrio porphyrio) iNHABITING JAVA WETLANDS