As a step toward understanding the structure and function relationships of phospholipases A2 (PLA2s), we isolated and sequenced five cDNAs encoding Trimeresurus flavoviridis (Habu snake) venom PLA2 isozymes. Comparison of the nucleotide sequences of these cDNAs revealed that the homologies of the 5′ and 3′ untranslated regions were much higher than that of the protein-coding regions and that the base substitution rates at the first, second, and third position of codons are similar in the coding region. To gain further insight into this novel findings, six T. flavoviridis venom gland PLA2 isozyme genes were isolated and sequenced. They were found to consist of four exons and three introns. The numbers of nucleotide substitutions per site (KN) for introns are approximately one-fourth of the numbers of nucleotide substituions per synonymous site (KS) for the protein-coding regions, indicating that the introns are unusually conserved. The fact that the numbers of nucleotide substitutions per nonsynonymous site (KA) are close to or larger than KS values for relevant pairs of genes revealed that Darwinian-type accelerated substitutions have occurred in the protein-coding regions of exons. This is compatible with the presence of PLA2 species with diverse physiological activities in the venom.