Diagnosis: Modal fin-ray counts of D-VI,11 A-10 and Pect-18-20 indicate Coryphopterus punctipectophorus. Most other sand-goby congeners have 10/10, with only a rare individual with 11 second-dorsal-fin elements. The distinguishing features of adult C. punctipectophorus are mostly not present on recruits and small juveniles.
Analogues: The sand goby clade share morphology and most markings as larvae and new recruits. C. punctipectophorus can best be separated by fin-ray counts (11/10) at these early stages. C. punctipectophorus and the other head-striped sand gobies develop short stripes on top of the head very early in transition, separating them from the spotted-head gobies (i.e. C. eidolon, C. thrix, C. alloides, C. kuna, and the non-sand Coryphopterus species).
