Abstract
This study investigated genetic diversity of the giant tiger shrimp (Penaeus monodon), an economically important penaeid species in Indonesia, using 558 base pairs of the mitochondrial cytochrome c oxidase Subunit I (COI) gene. A total of 10 samples were collected from three populations throughout Indonesia and three samples were taken from hatchery. The mitochondrial COI results found high levels of genetic differentiation. From Bayesian tree building method there were two clades on phylogenetic tree with high posterior probability value 1.00. COI mt-DNA analyses revealed that there were six haplotypes in which four haplotypes in clade A and two haplotypes in clade B. Divergences of COI between two clades showed an average 6.9% (range=6.7%-7.6%), while genetic distance within clade A 0.2% (range=0-0.5%) and within clade B 0.3% (range=0-1.1%). Results from this study suggest the occurrence of two cryptic species in the Penaeus monodon from Indonesia.
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