A survey of the malaria vectors in an area is a critical component of an effective vector control strategy. This study aimed to investigate the malaria vectors in four communities of Southern Gombe, Northeastern Nigeria. A total of 3200 adult female Anopheles reared from larvae in the four communities from two Local Government Areas (LGAs) in Southern Gombe were identified. Anopheles pretoriensis were dominant 1662 (51.9%) followed by An. gambiae sl 868(27.1%), An. maculipalpis 267(8.3), An. rufipes 252(7.9) and An. coustani 10(0.3%), and the least were An. pharoensis 6(0.2%). The remaining 135(4.3%) were unidentified. Of the 262 An. gambiae sl identified by species-specific PCR method, 135(51.5%) were found to be An. coluzzii, 60(22.9%) An. gambiae and only 1(0.4%) was An. arabiensis whereas hybrid constitutes 16(6.1%).To determine significant differences in species composition, the results from the four study sites were pooled together. Anopheles pretoriensis was significantly different from all the other species identified (p = <0.0001 -0.0454). An. gambiae sl. was significantly different from An. coustani and An. pharoensis (p = 0.0258, 0.0249 respectively). There was no significant difference between An. maculipalpis, An. rufipes, An. coustani and An. pharoensis (p = 0.9261 ->0.9999). There was a significant difference between the number of species identified as An. coluzzii and An. arabiensis (p = 0.0025). But there was no significant difference between An. coluzzii and An. gambiae (p = 0.1212). The heterogeneity and sympatry of Anopheles species observed is a threat to malaria control as the secondary vectors have behaviour that evades the current vector control interventions. It is expedient to re-strategize the vector control interventions in the study area.