Mallomonas guttata species complex was investigated in a tropical region using electron microscopy and molecular phylogeny. A study of six algal cultures belonging to the M. guttata morphotype revealed two main clades based on two datasets (SSU rDNA+ rbc L cpDNA, and ITS rDNA). This work establishes the phylogenetic position of M. guttata for the first time. We propose the new species, M. monilifera sp. nov. , for organisms from the second clade, which were distinguished by the presence of a rim around the pits located on the shield on their scales and showed considerable genetic distances from the M. guttata clade. Within this new species, the strains formed two subclades, for which we propose two subspecies. Scales of the new species were also found in several water bodies on Mindanao Island (Philippines).