It can be diagnosed from Lates calcarifer by the following characters: lesser body depth (26.6?27.6% SL, vs. 28.9?34.6% SL); 5 rows of scales between the base of the third dorsal-fin spine and lateral line (vs. 6); 31?34 serrae on the posterior edge of the preoperculum (vs. 16?26); third dorsal-fin spine 3.0?3.5 times the length of the second (vs. 2.1?2.8). It can be distinguished from Lates japonicus by having the third anal-fin spine longer (vs. shorter) than the second and possessing 5 (vs. 7) rows of scales between the base of the third dorsal-fin spine and the lateral line, a lesser body depth (26.6?27.6% SL, vs. 30.3?33.7% SL), and 47?52 (vs. 58?63) lateral-line scales. It differs from Lates uwisara by having a greater eye diameter (5.5?5.6% SL, vs. 4.4?4.7% SL), a lesser body depth (26.6?27.6% SL, vs. 28.4?34.5% SL), a shorter dorsal-fin base (41.1?43.2% SL, vs. 43.3?45.0% SL), and by possessing 5 (vs. 7) rows of scales between the base of the third dorsal-fin spine and lateral line (Ref. 90099).