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We performed a comparison of molecular and morphological diversity in a freshwater colonial genus Synura (Chrysophyceae, Stramenopiles), using the island of Newfoundland (Canada) as a case study. We examined the morphological species diversity in collections from 79 localities, and compared these findings to diversity based on molecular characters for 150 strains isolated from the same sites. Of 27 species or species‐level lineages identified, only one third was recorded by both molecular and morphological techniques, showing both approaches are complementary in estimating species diversity within this genus. Eight taxa, each representing young evolutionary lineages, were recovered only by sequencing of isolated colonies, whereas ten species were recovered only microscopically. Our complex investigation, involving both morphological and molecular examinations, indicates that our knowledge of Synura diversity is still poor, limited only to a few well‐studied areas. We revealed considerable cryptic diversity within the core S. petersenii and S. leptorrhabda lineages. We further resolved the phylogenetic position of two previously described taxa, S. kristiansenii and S. petersenii f. praefracta, propose species‐level status for S. petersenii f. praefracta, and describe three new species, S. vinlandica, S. fluviatilis, and S. cornuta. Our findings add to the growing body of literature detailing distribution patterns observed in the genus, ranging from cosmopolitan species, to highly restricted taxa, to species such as S. hibernica found along coastal regions on multiple continents. Finally, our study illustrates the usefulness of combining detailed morphological information with gene sequence data to examine species diversity within chrysophyte algae.

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Mallomonas distinguenda sp. nov. and Mallomonas skvortsovii sp. nov. are described from Dak Lua swamp, located in Cat Tien National Park (Dong Nai Province, Southeastern Viet Nam). The description is based on silica-scale morphology studied by means of transmission and scanning electron microscopy. These species belong to the section Papillosae based on scale morphology. The most characteristic feature for both taxa is the shield reticulation. In the case of Mallomonas distinguenda, it is an external reticulation. By contrast, Mallomonas skvortsovii has internal reticulation.

The silica-scaled chrysophyte flora from Indonesian Papua was investigated by means of electron microscopy. A total of twenty-four taxa were recorded, including five belonging to Paraphysomonas, one to Chrysosphaerella, one to Spiniferomonas, fifteen to Mallomonas and two to Synura. Thirteen taxa were recorded for the first time in Indonesia. Comparison of the species composition of silica-scaled chrysophytes from different parts of the Island of New Guinea shows significant differences. A “living fossil” was discovered, Mallomonas preisigii, which was described previously from Eocene deposits in Northern Canada. Although the scales from Papua slightly differ from those of the fossil one, we believe they belong to the same morphospecies. Mallomonas preisigii can be considered as a paleoendemic species.