The transforming protein of Rous sarcoma virus, p60src, the Abelson virus protein, p120, and the Y73 virus protein, p90, all have associated tyrosine protein kinase activities in vitro. Possible structural homology between these functionally related proteins was investigated by two-dimensional analysis of both methionine-containing and phosphate-containing tryptic peptides derived from biosynthetically labeled proteins. Marked differences were found between the maps of both [35S]methionine-labeled and 32P-labeled tryptic peptides. This suggests that the transforming gene of Rous sarcoma virus and the putative transforming genes of Abelson virus and Y73 virus are different. In addition, each of these genes has been shown previously to be unrelated to the putative transforming gene of Fujinami sarcoma virus, another virus which encodes a protein with associated tyrosine protein kinase activity. Therefore, it appears that there exist at least four distinct classes of functionally related RNA tumor viruses. Analysis of phosphorylated tryptic peptides did, however, reveal homology between one of the two phosphotyrosine-containing tryptic peptides of p90 of Y73 virus and the single phosphotyrosine-containing tryptic peptide of p60src of Rous sarcoma virus. Comigration of these two peptides in several different buffers and the identical mobility of their phosphorylated cleavage products after secondary digestion with protease V8 of Staphylococcus aureus indicated that p60src and p90 contain an identical site of tyrosine phosphorylation in vivo. The results are discussed with respect to the evolution of RNA tumor viruses which encode proteins with associated tyrosine protein kinase activities and the limitations of analysis of detecting homology between genes by both molecular hybridization and peptide mapping.