Code obfuscating technique plays a significant role to produce new obfuscated malicious programs, generally called malware variants, from previously encountered malwares. However, the traditional signature-based malware detecting method is hard to recognize the up-to-the-minute obfuscated malwares. This paper proposes a method to identify the malware variants based on the function-call graph. Firstly, the function-call graphs were created from the disassembled codes of program; then the caller–callee relationships of functions and the operational code (opcode) information about functions, combining the graph coloring techniques were used to measure the similarity metric between two function-call graphs; at last, the similarity metric was utilized to identify the malware variants from known malwares. The experimental results show that the proposed method is able to identify the obfuscated malicious softwares effectively.