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 A₂ (PLA₂), 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 PLA₂ 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 PLA₂3 from D. r. russellii and CTX7 from N. naja were determined. Additionally, the polymorphic amino acid residues of PLA₂3 were preferentially localized on the potential antigenic sites. While 2 types of PLA₂ (N and S types) were found in D. r. russellii (India) and D. r. siamensis (Java), all the PLA₂s from D. r. siamensis (Burma) were N type, and those from D. r. russellii (Sri Lanka) were primarily S type.