In recent years, fluorescence microscopy has revitalized the study of invertebrate comparative morphology. Here we explore the usefulness of combining confocal laser scanning microscopy (CLSM) and cuticular autofluorescence to examine the taxonomically challenging marine planktonic “y-larvae” (Pancrustacea: Facetotecta). To gauge the effectiveness of CLSM with autofluorescence in producing taxonomically useful images, we applied it to seven distinct y-naupliar species or morphospecies that had previously undergone scrutiny by other techniques. The specimens were part of a museum collection of glycerin-jelly slides of exuviae of last-stage y-nauplii, a key instar for studying the taxonomy of y-larvae. For Hansenocaris demodex, the level of detail obtained from a single specimen was comparable to that previously obtained by scanning electron microscopy (SEM). For Hansenocaris aquila, revisiting the original holotype specimen resulted in a dramatic increase in our understanding of the species’ morphology, including taxonomically pivotal information about its spinose labrum and a digitally rotated lateral view. CLSM analyses of the other five specimens, which represented a broad spectrum of y-naupliar morphology, efficiently generated more such information. Novel observations were made concerning putative external rudiments of both the first and second maxillae in late nauplii as well as the extreme dorso-ventral flattening of some naupliar types. CLSM observation of museum slides of naupliar exuviae using cuticular autofluorescence thus shows great promise of becoming an excellent tool for studying the morphology and taxonomy of y-larvae, and we suggest that this technique might also profitably be applied to other forms of larval exuviae.