Botnet, a network of computers that are compromised and controlled by the attacker, is one of the most significant and serious threats to the Internet. Researchers have done plenty of research and made significant progress. As the extensive use and unique advantages of peer-to-peer (P2P) technology, the new advanced form of botnets with the P2P architecture have emerged and become more resilient to defense methods and countermeasures than traditional centralized botnets. Due to the underlying security limitation of current system and Internet architecture, and the complexity of P2P botnet itself, how to effectively counter the global threat of P2P botnets is still a very challenging issue. In this paper, we present an overall overview and analysis of the current defense methods against P2P botnets. We also separately analyse the challenges in botnets detection, measurement and mitigation in detail which introduced by the new form of P2P botnets and propose our suggestions to corresponding challenges.