The notorious difficulties encountered in species identification of bivalve larvae through morphological characters have given rise to several alternative molecular approaches. In the present work, we propose a method based on PCR-SSCP combined with sequencing of partial 18S rDNA region, in which a large number of larvae can be scored and species identified with minimum sequencing effort. A primer set was developed to amplify a taxonomically informative 18S region of fragment size suitable for high resolution PCR-SSCP. The method developed is fast processing and has the potential of identifying most species present in a plankton sample with low economic efforts. Those species for which partial 18S sequences are not yet available from GenBank, can be identified in families or at higher categories. The method was also tested on nine species and two subspecies of commercial importance in Italy to be carried out by the use of PCR-SSCP alone without sequencing.