The genealogical relationships in the green algal genus Microspora (Chlorophyceae) are determined by phylogenetic analysis based on 15 ecological, morphological and reproductive characters. It is found that the traditional defining characters like cell shape and distinctness of the H-shaped pieces (composing the cell wall) play a major role in rooting of the cladograms and that species – forming a prominent rope-like growth habit in rapid streams – are closely related. It is suggested that the pH value of the habitat proves to give a more substantial phylogenetic signal than the type of water movement.