The proteins of 91 strains of Mycoplasma from 19 established species and three groups of uncertain taxonomic position were separated by two-dimensional polyacrylamide gel electrophoresis. Considerable variations in protein patterns were found among strains from the same species or subspecies; the percentage of matching spots (% of congruence) ranged from 42%–100%, but many proteins were strongly conserved in all strains of a given species. Maps of these conserved proteins could be used to identify strains. It was concluded that (1) large colony-type strains of Mycoplasma mycoides subspecies mycoides are more closely related to M. mycoides subspecies capri than to small colonytype strains of M. mycoides subspecies mycoides; (2) Mycoplasma capricolum, Leach group 7, and the F38 group of mycoplasmas are all related to M. mycoides; (3) the 2D group of strains are not related to either M. mycoides or Mycoplasma bovis, (4) M. bovis and Mycoplasma agalactiae are closely related; (5) apart from a small overlap in pattern between Acholeplasma laidlawii and Acholeplasma granularum, the type strains of seven established species of Acholeplasma each had distinct protein patterns that justified their classification as separate species; and (6) analysis of two-dimensional protein patterns is a valuable method for resolving problems in mycoplasma taxonomy and for identifying strains.