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Asian sebass, barramundi, Lates calcarifer (Perciformes, Latidae) was first described in 1790 by the name of Holocentrus calcarifer by Bloch. The name of genus Lates by Cuvier & Valenciennes (1828) was given to comprise other species, including Nile perch (L. niloticus). Lates calcarifer is a type of fresh-seawater fish that has high economic value comparable to salmon and tuna. The population of Asian seabass in Australia, Myanmar, Sri Lanka and Japan was reported in different types. Lates lacdiva from Sri Lanka had a lower height than L. uwisara (Myanmar) and L. calcarifer (Australia). However, the attempt to describe and assess the diversity of Lates in Indonesia, including in the Bone Bay and Makassar Strait have never been done. This study analyzed the morphology and genetic diversity of barramundi caught in the Bone Bay and Makassar Strait waters as an effort to document and map species richness. Both morphological and genetic diversity of barramundi caught in both sites were low. The body was elongated with black caudal-fin. Barramundi from Bone Bay had a white-silver color, while those from the Makassar Strait were greenish in color. Dorsal-fin was divided in two parts with base of second dorsal fin less than that of first dorsal-fin. Third dorsal-fin spine longest. Dorsal-fin spines of Asian seabass from the Makassar Strait were more varied than that Bone Bay. Anal-fin spines of Asian Seabass from Bone Bay were varied than that Makassar strait with third anal-fin spine longest (III>II>I). The pectoral-fin was shorter than the pelvic-fin. The pelvic-fin did not reach the anus and generally separate, but in some specimens are fused by a thin membrane. Caudal-fin was rounded and consisted of 15-18 weak spines. Body height was 29.30- 33.35% to standard length (SL), with certain specimen was found with height up to 37.50% from SL. One small spine in the operculum with a position above the lateral line, and 4-5 small spines at the bottom of the pre-operculum. The highest genetic distance was 0.16% while the number of haplotypes was two with 0.00045 nucleotide diversity.