Seven scale-bearing species of prasinophyceans (Chlorophyta) were studied in light and electron microscopy, pigment analysis, and molecular analysis of the small subunit (SSU) rDNA. Unialgal cultures were obtained from samples collected in the Nervión River estuary, Gulf of Biscay, Spanish Atlantic coast. Five of the species belong to the genus Pyramimonas (Prasinophyceae, Pyramimonaceae) and one each to the genera Mamiella (Mamiellophyceae, Mamiellaceae) and Nephroselmis (Nephroselmidophyceae, Nephroselmidaceae). The morphological features of all the strains analyzed agreed closely with the phylogenetic analysis, which in the case of the genus Pyramimonas presented several clusters corresponding to the subgenera Vestigifera (Pyramimonas orientalis, Pyramimonas moestrupii), Punctatae (Pyramimonas robusta), Pyramimonas (Pyramimonas propulsa), and Trichocystis (Pyramimonas grossii). Even though the phylogenetic relationship among these subgenera remains unclear, the results suggested that the Punctatae should remain an independent clade at least until more sequences or genes are analyzed. According to their accessory pigment composition, three groups were distinguished after their pigment ratios were calculated: prasinoxanthin-containing (Mamiella gilva), loroxanthin ester-containing (P. grossii and P. moestrupii), and siphonaxanthin-containing strains (Nephroselmis pyriformis and remaining Pyramimonas species). A high intraspecific variability was found, which highlights the need of an indepth analysis and multiple technique approach to ensure accurate identification of nanoplanktonic microalgae.