To examine the molecular diversity of the venom proteins of the Russell's viper (Daboia russellii russellii) and the Indian cobra (Naja naja) in Sri Lanka, we isolated 38 venom proteins through a combination of anion exchange chromatography followed by reversed-phase high performance liquid chromatography. From the venom of D. r. russellii we isolated 15 proteins: 5 isozymes of phospholipase A(2) (PLA(2)), 4 serine proteases, 2 C-type lectin-like proteins, 2 L-amino acid oxidases, 1 cysteine-rich secretory protein (CRISP), and 1 metalloproteinase. From the venom of N. naja we isolated 23 proteins: 10 isoforms of cytotoxins (CTX), 7 PLA(2) isozymes, 2 muscarinic toxinlike proteins, 2 CRISPs, 1 nerve growth factor, and 1 new thrombin-like serine protease. Most of these proteins contained new amino acid sequences for each species, indicating molecular diversity in venom proteins. The entire amino acid sequences of PLA(2)3 from D. r. russellii and CTX7 from N. naja were determined. Additionally, the polymorphic amino acid residues of PLA(2)3 were preferentially localized on the potential antigenic sites. While 2 types of PLA(2) (N and S types) were found in D. r. russellii (India) and D. r. siamensis (Java), all the PLA(2)s from D. r. siamensis (Burma) were N type, and those from D. r. russellii (Sri Lanka) were primarily S type.