Understanding the dispersal dynamics of molluscan larvae is crucial for population structure analysis, population dynamics assessment, and effective management of exploited or declining species. Traditional methods of larval identification rely on morphological analysis, labor-intensive and costly. Alternatively, DNA analysis has been used for molluscan larval identification, but the quantification of larvae using molecular methods remains unclear. In this study, a molecular identification method for Semimytilus algosus larvae in field samples, along with a quantitative approach cross-validated with microscopy counting are presented. The quantitative proficiency of the method was evaluated using subsamples of known larval quantities, showing a high correlation between PCR results and larval count, but when blind field samples were quantified, the correlation was lower. Although this method may not replace larval counting by microscopy, it provides quantitative information about total larval DNA that could be considered in the future as a relevant predictor for settlement.