Twelve cDNA clones were generated, covering approximately 95% of the cowpea mottle virus (CMeV) genome from the 3' end to near the 5' end. The entire capsid protein sequence of 1,104 nucleotides was contained in two clones located near the 3' terminus. The codons represented 367 amino acids (M(r) 39,611). The postulated amino acid sequence of CMeV capsid protein had 36% homology to turnip crinkle virus and 26% homology to carnation mottle virus in the arm and S domains, but western blots showed no serological relationship to either. On the basis of the organization and expression of its genome and its physicochemical properties, CMeV is assigned to the carmovirus group. Like other carmoviruses, CMeV generates three dsRNAs which are co-terminal at the 3' end in infected tissues, but CMeV differs from other carmoviruses in the absence of encapsidated subgenomic RNAs.