Marine invertebrate larvae represent a transitory, but nonetheless important component of planktonic communities. Assessing their contribution to plankton diversity has been hindered by numerous methodological difficulties, notably at the identification step. For many sessile invertebrates, planktonic larvae also play a crucial role, as they are their sole dispersal vectors. Understanding connectivity patterns among marine populations is fundamental for managing coastal ecosystems and their associated resources. Indirect approaches, relying on population genetics models, have widely contributed to elucidate population structure and gene flow patterns, but show, in some cases, conflicting results with larval dispersal potential. In an attempt to facilitate surveys of larval distributions and abundances, an in situ hybridization on whole larvae method was tested over a range of marine invertebrate larvae collected from environmental plankton samples. Ribosomal RNA-targeted oligonucleotide probes were used for hybridization, followed by a colorimetric reaction allowing signal detection at the light microscope. Promising results were obtained, showing an unambiguous positive hybridization signal with a eukaryotic (positive) probe, but no signal with a negative probe. Using species-specific probes, the method could be applied to resolve key current questions in marine ecology, addressing both wide and fine scales.