Paraphysomonas vestita is a unicellular, colorless, silica-scaled chrysophyte that plays an important ecological role in freshwater microbial communities as a consumer of prokaryotic and eukaryotic prey. There is little biogeographical information for this minute protist despite its significant role in aquatic food webs. In addition, the phylogenetic relationship of P. vestita to other taxa is unclear as P. vestita may be polyphyletic or a cryptic species complex. In this study, a clonal isolate from a freshwater sample of Laguna de Bay, Philippines was subjected to morphological study by electron microscopy and its small subunit ribosomal RNA (SSU rRNA) gene was sequenced. Morphological studies showed that the isolate possesses two unequal flagella emerging from the anterior part of the cell. Negative staining revealed the structure of the scales which consist of a baseplate with slightly thickened rim. The narrowing spine arises from the center of the baseplate. These results agree with previously studied isolates of P. vestita. The 18S rRNA gene sequence of the isolate had a very high similarity (99%) to P. vestita strain PV10. Phylogenetic analysis also showed that the isolate clustered with other Paraphysomonas sequences with high bootstrap support. Phylogenetic studies confirmed that P. vestita may be polyphyletic. No studies on the ultrastructure and phylogeny of a silica-scaled chrysophyte isolated in the Philippines have been reported so far. Results from this study may contribute to further ultrastructural and phylogenetic studies on aquatic flagellates and specifically to a revision of this potentially polyphyletic species.