DNA sequence and restriction-site-associated DNA sequencing (RADseq) databases were used to perform Rhynchocinetes durbanensis genotyping using a next-generation sequencing (NGS) platform. Ten simple-sequence repeat (SSR) markers and 429,078 single-nucleotide polymorphism (SNP) loci were identified for the analysis of genetic diversity among wild and farmed R. durbanensis populations. The genetic differentiation index (Fst) for the SSR analysis between the wild and farmed populations was 0.0184, and population structure analysis using Bayesian inference indicated no significant genetic differentiation. A total of 162,109 specific SNP alleles were identified within the farmed population, which were fewer than the number identified in the wild population, which contained 194,579 specific SNP alleles. Homozygosity within the farmed population was higher than that for the wild population. A maximum-likelihood phylogenetic tree separated the farmed and wild samples into 2 groups. However, p-value analysis did not reveal significant differences between farmed and wild samples. The Fst value inferred by SNP analysis between the two populations was 0.087, indicating no significant differentiation