SDS-PAGE profiles of whole cell proteins were used to differentiate among 13 Azolla accessions belonging to six species in section Euazolla. Azolla mexicana, A. microphylla, A. rubra, A. filiculoides and A. caroliniana showed highly identical protein profiles except A. caroliniana 3001, in which two distinct bands of molecular weight 81 kDa and 97 kDa were absent. This can be a useful marker for distinguishing this strain among accessions belonging to section Euazolla. The protein profiles of two accessions of A. pinnata, placed in section Rhizosperma consisted of unique bands in the range of 12-17 kDa, which were absent in all species of section Euazolla. The distinct SDS-PAGE profile, especially those of A. caroliniana and A. pinnata, provide useful fingerprints for identification of strains belonging to these species among mixtures.