Abstract:The small abalone, Haliotis diversicolor, is an economically important shellfish species in East Asia. The wild stocks have been highly threatened due to overfishing in the past several decades. Taking into account conservation and recovery of wild resources, long preserved samples were used to analyze population structure. However, extreme fragmentation of DNA limited the use of these degraded DNA samples. In this study, a total of 96 novel single nucleotide polymorphisms (SNPs) were identified based on transcriptomes of H. diversicolor. The parallel target sequencing was then used to examine one wild population collected in 2003 from Sanya Bay, Hainan Province with degraded DNA. Nineteen loci appeared in more than 80% of individuals and were polymorphic. This study provides a valuable method for using degraded DNA and molecular markers for genetic diversity analysis of H. diversicolor.