Genetic diversities of Anopheles gambiae ss and Plasmodium falciparum is a major challenge in malaria control as it affects the vector, treatment and production of a vaccine. The aim of the study is to identify the genetic variabilities of A. gambiae ss using the A. gambiae species-specific multiplex Polymerase Chain Reaction (PCR) and P. falciparum using merozoite surface protein (msp2) as antigenic marker. Results revealed that the A. gambiaes ss identified were of the M-forms and the two families of msp-2, FC27 and 3D7 were observed among the isolates of P. falciparum. Eleven (11) number of genotypes were recorded with FC27 having the highest frequency of 8(26.67%) while 3D7 had the least number of genotypes encountered with 3(10%). The allelic frequency of FC27 type was higher 29(96.67%) than 3D7 alleles with 26 (86.67%). There is no significant difference found in the distribution of FC27 alleles and 3D7 alleles in the study populations (p>0.05). The observed population genetics of A. gambiae ss and P. falciparum is likely to be a consequence of the high transmission intensity. This has important implications for malaria control strategies and vaccine production.Keywords: Genetic veriabilities; malaria control strategy.