Tomistoma schlegelii is an endangered crocodilian with an adult population size less than 2,500 individuals. To make appropriate in situ and ex situ conservation strategies, it is essential to perform parentage assignment for breeding captive populations and to conduct population study in wild populations based on genetic data. However, there is no suitable genetic marker available for T. schlegelii. Here, we reported 18 novel microsatellite loci from the tomistoma. Allele numbers of these loci ranged from 2 to 16, and their observed heterozygosity ranged from 0.105 to 0.684. The probability for excluding false parental pairs using the 18 loci was 99.9999 %. These markers are useful not only in parentage assignment but also in population structure analysis.
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