The question of whether pathogenic 'P' and nonpathogenic 'NP' isolates of E. histolytica constitute one or two species was examined using isoenzyme analysis and 'riboprinting.' A strict correlation between isoenzyme and riboprint patterns was observed for the two forms. Attempts to interconvert the forms failed to produce an alteration in either the isoenzyme or riboprint pattern. Partial sequence analysis of cloned ribosomal RNA genes detected differences at approximately 2% of 780 bases compared. Primers synthesized to specifically amplify 'P' rDNA did not detect 'P' rRNA genes in the 'NP' genome ruling out the possibility a single 'P' rRNA gene is amplified during 'NP' to 'P' conversion. We conclude the reported interconversion of 'NP' to 'P' forms of E. histolytica is artifactual and the forms represent distinct species. The use of riboprinting for identification and phylogenetic analyses of other protozoa was examined using the trypanosomatid genus Crithidia. Data obtained showed the technique to be of phylogenetic value revealing a coevolution of host and parasite groups, and an unexpected close relationship between the genera Crithidia and Leishmania. Sargeaunt, on the basis of the electrophoretic analyses of four isoenzymes, divided E. histolytica into 22 zymodemes. We examined several of his cloned isolates said to represent 7 zymodemes and found them to fall into three zymodemes. We have evidence the discrepancies between our data and those of Sargeaunt's are due to his failure to use adequate bacterial controls and as a result misinterpreted many of the bacterial bands as amebal in origin. Separation of large chromosome-like DNA molecules from E. histolytica was achieved by pulse field electrophoresis. At least nine distinct bands were observed with the largest comigrating with Malaria chromosome XIV (3.2 Mb). Identification of the chromosomes and mapping is currently being studied by hybridization with a number of cloned E. histolytica genes.