Protobothrops mucrosquamatus, also known as the habu, is a major venomous species causing viper snake evenomings in Pan-Asia. A study in Taiwan recorded 250 habu envenomings annually, which accounts for approximately 23% of total snakebites. Habu contains a high abundance of necrotic and hemorrhagic toxins that can induce local inflammation, hemorrhage, necrosis and edema in snakebite victims. Administration of antivenom has been recommended for therapeutic treatment; however, the therapeutic effect might vary with venom composition. A further proteomic analysis on individual habu snake venom is required to identify the toxin variants which might affect the neutralization efficacy of antivenom. In the study, venom was collected from a total of 34 individual habu snakes from various regions in Taiwan, and venomic results revealed that there is a wide dynamic range in the composed snake venom metalloproteinases (SVMPs) and phospholipases A2 (PLA2s). In addition, there are four PLA2 variants identified from these geographic samples, which can be markers to identify the putative subspecies of habu from various regions in Taiwan. We conclude that venomic analyses of intra-specific variation of proteomic profiles of snake venoms can provide useful information for better snakebite management.