Description: Body thin, long, and narrow with a large eye and relatively small somewhat downturned mouth. Pectoral fins medium length, pelvic fins medium length and fused with a clear frenum, dorsal and anal-fin bases long, caudal peduncle relatively long and somewhat narrow. Pretransitional larvae have melanophores only on the dorsal fins, along the membranes between the dorsal-fin spines and the first three or four second-dorsal-fin elements (these can be missing on larvae with frayed fins). Series of transitional larvae show the eye remaining large and round, often with a prominent dorsal, occasionally a ventral, indentation in the iris. Transitional larvae develop a melanophore on the proximal middle pectoral-fin rays and rows of large melanophores on the body near the base of the dorsal fins. The characteristic comma-shaped bar below the eye then develops from the iris down and a corresponding bar develops on the upper iris onto the dorsal surface of the head. Leukophore patches form over the top of the head and over the iris, on the cheek, and on the base of the pectoral fin.
Analogues: (long, and narrow, no anal-fin base row of melanophores) Similar median-fin ray counts occur in Bollmannia litura, but that genus has seven first-dorsal-fin spines and many more pectoral-fin rays (20 or more). Rare individuals of Ctenogobius saepepallens , and probably others of that genus, can have equal numbers of anal and second-dorsal-fin ray elements and thus match the counts of this larval type. Most long, and narrow larval gobies have a row of melanophores along the anal-fin base, but among some groups there are often individuals without markings (primarily Ctenogobius spp. and Evorthodus lyricus). Those individuals can resemble larval Gnatholepis thompsoni, but usually have one more anal-fin element than second-dorsal-fin elements vs. equal numbers in Gnatholepis thompsoni larvae. In addition, larval Gnatholepis thompsoni have a distinctly larger eye, a smaller downturned mouth, and melanophores along the dorsal fins. The transitional melanophore patterns are also completely different. Larval Evermannichthys spp. have a larger mouth, a sharply-pointed snout, and spiny caudal peduncle scales.
Diagnosis: Modal fin-ray counts of D-VI,12 A-12 Pect-17 indicate Gnatholepis thompsoni. (DNA)