Identification of organism species can be done by morphometric analysis and molecular identification such as DNA sequencing. Morphometric analysis provide an overview of the habitat conditions of Asian moon scallops (Amusium pleuronectes) while molecular identification strengthen the morphometric analysis. This study provided the first report of molecular identification and morphometric analysis of Asian moon scallops in Bone Bay and the Makassar Strait waters. Genetic test samples were taken from adductor tissue which were then preserved using alcohol at the next stage. Morphometric analysis was carried out by analyzing the relationship between shell length (cm) and shell weight (g) using a regression test. DNA sequencing results were analyzed using MEGA 10 software, which included BLAST, Haplotype, genetic distance analysis, and phylogenetic tree. The results of morphometric analysis showed that A. peluronectes in the waters of Bone Bay and Makassar Bay had a negative allometric growth pattern (b<3) and a coefficient of determination (R) <60%, meaning that there was a close relationship between length and weight. The same growth pattern was influenced by habitat conditions such as temperature, substrate, and depth at both sampling locations which tended to be the same. Analysis of the genetic distance of Asian moon scallops obtained in the waters of Bone Bay and the Makassar Strait ranged from 0.001 to 0.006, indicating a low genetic distance. This finding concludes the phylogenetic tree analysis demonstrated that the genetic variations in Asian moon scallops were closely related.