Eukaryotic picophytoplankton (EPP) play vital roles in primary productivity and biogeochemical cycling in the marine environment. In this study, we explored the diversity of EPP communities in two different embayments and the shifts in their community structuring during monsoonal reversal in the northwestern Philippines. Water samples were collected weekly from late northeast (NE) monsoon to intermonsoon (IM) or summer periods (February–April 2019) in Bolinao, Pangasinan, and once in January in Masinloc, Zambales. EPP community profiling was done through targeted sequencing of the V4 region of the 18S rRNA gene. Grouping of samples based on physicochemical parameters was consistent with that of community beta diversity, suggesting strong clustering between late NE and IM periods. This exhibits short- term community shifts of EPPs possibly associated with the monsoonal transition. Specifically, overall EPP alpha diversity increased towards summer coupled with increased temperature and lower nutrient concentrations. NE monsoon samples from Bolinao and Masinloc were dominated by Chlorophyta and Stramenopiles, while Prymnesiophyta, Rhizaria, and Picozoa dominated the IM period samples in Bolinao. Specifically, the prasinophytes (Chlorophyta) Ostreococcus and Nannochloris distinguished the late NE communities of Masinloc and Bolinao, respectively. Phylogenetic analysis of dominant photosynthetic EPP further revealed the presence of Clades B5 and A1 of Micromonas, as well as Clades B and E of Ostreococcus. Tree topology of Ostreococcus diversity suggests the presence of a clade distinct from other established clades, possibly indicating novel diversity in the West Philippine Sea. This is the first report of these major picophytoplankton in Philippine waters, suggesting their significance and potential “hidden” diversity, which warrants further studies.