The aim of this study was to reveal the taxonomic position and phylogenetic relationships of the dominant planktic algae in two acid metal-rich lakes of different origin (Hromnice Lake and Plešné Lake, Czech Republic) and to investigate their morphology and ultrastructure under natural and laboratory conditions. Phylogenetic analyses (18S rRNA and ITS-2) revealed that the strain isolated from Hromnice Lake belongs to the species Coccomyxa elongata, while Coccomyxa from Plešné Lake was described as a new species C. silvae-gabretae. It is the first evidence that representatives of this genus are capable of becoming the dominant primary producers in the extreme environment of acid lakes with an increased supply of phosphorus. There were clear differences in cell morphology under different growth conditions, revealing the high phenotypic plasticity of the strains. The ability to change the morphology may help the cells of Coccomyxa to survive harsh conditions in the aforementioned acid lakes.