Scalloped spiny lobster (Panulirus homarus, Palinuridae) is an economically and ecologically important food species. Population structure of the scalloped spiny lobster across the southern coast of Sri Lanka (SCSL) (in Indian Ocean) was investigated using mitochondrial DNA (mtDNA) markers. Four sites belonging two regions were sampled (Hikkaduwa, Weligama in the southwest and Godawaya, Kirinda in the southeast) and DNA was isolated from tissues of pereiopod and used for PCR amplification. Genetic variation in DNA sequences were examined for two mtDNA gene regions; Cytochrome Oxidase I (COI) and Cytochrome B (CytB). High levels of haplotype diversity and nucleotide diversity were detected in all populations and estimated average fixation index (-0.026285 (p< 0.01)) indicated essential homogeneity among population. Results of AMOVA analysis confirmed an absence of signi?cant population structure among sites. Tests of neutral evolution and analysis of mismatch distribution suggested that P. homarus populations across the SCSL might have experienced a recent population expansion. Information emerged from the current study could be utilized when people design appropriate management strategies for conserving this vital wild marine resource.