Complementary DNA clones corresponding to the 3' terminus of sweetpotato feathery mottle virus (SPFMV) strains RC and C were synthesized and sequenced. An open reading frame followed by a 3' terminal non-coding region of 222 nucleotides and a terminal polyadenylation track was present in clones from both strains. Putative N-terminal capsid protein cleavage sites were identified for both strains 945 nucleotides 5' of the first stop codon. Sequence comparisons of these strains show 98% nucleic acid identity in the last 351 nucleotides of the capsid protein cistron and 100% in the corresponding amino acids. This relatively short homologous sequence element near the C terminus is responsible for the wide spectrum hybridization among SPFMV strains using in vitro transcribed antiviral RNA probes (riboprobes). The sequence similarity in the remaining N terminal 645 nucleotides is only 62% and 65% for their predicted amino acids. A tendency of decreasing nucleotide mismatches in the alignment from 5' to 3' end of both capsid protein cistrons was detected. Although the alignment of the predicted amino acid sequence of the SPFMV-RC capsid protein with those of other potyviruses showed significant homology, hybridization with riboprobes from both the 5' and 3' regions of the capsid protein cistron of SPFMV was virus-specific.