Mobile adhoc networks (MANETs) poses a large area of challenges in the field of security, this is due to the lake of infrastructure and the continuous changing in the network topology. Botnets are believed to be the most harmful danger that threatens any type of networks; because it controls the units in a non noticeable manner so detection of botnets is more difficult . in this paper the Artificial Immune System (AIS) is used as the defense system to the MANET to face botnets. Experimental results show that the use of fuzzy based security can enhance the security of AIS in MANETs