The monocled cobra (Naja kaouthia) and equatorial spitting cobra (Naja sumatrana) are two medically important venomous snakes in Southeast Asia. Proteomics and toxicity studies established that alpha-neurotoxins are invariably the principal lethal toxins in their venoms. The cytotoxins (cardiotoxins, CTX), on the other hand, are much complex functionally and structurally. We investigated the venom gene complexity of the cobras through de novo venom-gland transcriptomics, and showed that cytotoxin genes were the most abundantly and diversely expressed. The CTX were classified into P-type or S-type CTX based on the presence of Pro31 or Ser28 amino acid in the sequence accordingly. To further characterize their pharmacological properties, the CTX were purified from the venoms through sequential high-performance liquid chromatography, validated with nano-liquid chromatography-tandem mass spectrometry, and investigated for their cytotoxic effects in vitro and in vivo. The P-type and S-type CTX exhibited differential cytotoxicity, consistent with the variable degree of hydrophobicity in the membrane-binding loop of the toxin molecule. Protein antigenicity was, nevertheless, conserved among the cobra cytotoxins, and this enabled cross-reactivity and cross-neutralization activity of cobra antivenom. The cobra cytotoxins, however, were phylogenetically and immunologically divergent from cytotoxin-like proteins of the Asiatic coral snakes (Calliophis spp.), whose cytotoxins form a distinct clade of three-finger toxins with distinct evolutionary implications. Furthermore, the cobra cytotoxins demonstrated high anti-proliferative activities in breast, prostate and lung cancer cell lines, with promising selectivity noted in the latter. Future studies should aim to unleash the anticancer potentials of the cytotoxins.