We carried out interphylum protoplast fusion between Ochromonas danica and Haematococcus pluvialis using polyethylene glycol. Different enzyme mixtures were evaluated to prepare the protoplast of H. pluvialis; however, in the absence of a cell wall, O. danica was not treated with lytic enzymes. Maximum lytic activity of 57% was observed using proteinase K for 90 min. The heterofusants were easily identified by pigmentation of the hybrid colonies on BG11 medium. Fatty acid analysis in putative hybrids of O. danica and H. pluvialis confirmed the hybrid origin of these cells. Accordingly, the characteristic fatty acids of O. danica (C16:2 and C24:0) and H. pluvialis (C16:0 and C18:3n-6) were detected in the hybrid algae. These results indicated successful genetic recombination between the two microalgal phyla.