Algae represent a diverse polyphyletic consortium of ancient plants comprising different evolutionary lineages of mostly photoautotrophic organisms. The recent status of the systematics of algae is discussed. An overview about the main groups of algae including cyanobacteria inhabiting inland water bodies is given. The systematics of these algal groups is based on both conventional morphological characteristics and modern molecular phylogenetic considerations. The main characteristics of each algal group are described such as morphology of the cells, life form, ultrastructural criteria of the chloroplasts, the flagellar apparatus, and the pigment composition. The estimated numbers of taxa in each algal group are presented. In case studies, arguments for using a polyphasic approach in algal systematics and ecology are provided.