Marine phytoplankton forms the basis of the marine food web. Its diversity (size and pigmentation) has a significant impact on biogeochemical processes such as photosynthetic efficiency, trophic interactions, and global carbon fluxes. To date, little is known about the Algerian Basin regarding phytoplankton quality and quantity. In this study, we analyzed the distribution of phytoplankton communities in the Algerian Basin based on HPLC/Chemotaxonomy analysis for the summer season of 2014. The chemical taxonomy software CHEMTAX v1.95 was used to estimate the contributions of various phytoplankton groups to total chlorophyll a (TChl a). The results showed that prymnesiophytes were the dominant group (16%) in the nanoplankton and occupied the entire water column, whereas cryptophytes were observed exclusively in the western region of the basin, and contributed about 6% to the TChl a. Diatoms had the highest contributions (18%) to the TChl a, and their emergence was linked to nutrient enrichment. Dinoflagellates had a contribution of about 12% with little variation throughout the basin. Prochlorococcus had a contributions of about 13% and prevailed in the deep layers (60–100 m) following the nitracline, while Synechococcus (11%) occupied the shallower layers (10–60 m) (beneath the MLD) following the nutrient depletion. Moreover, it is noteworthy that phytoplankton communities in the western part of the basin showed greater diversity and abundance, influenced by Atlantic waters and deep nutrient enrichment. In contrast, the eastern part of the basin displayed lower productivity, characterized by reduced diversity and the prevalence of nano- and picoplankton.