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Background Anopheles arabiensis  is a member of  Anopheles gambiae  complex and the main malaria vector in Sudan. There is insufficient population genetics data available on  An. arabiensis  for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among  An. arabiensis  populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published  An. gambiae  microsatellite loci primers were used to amplify the DNA of  An. arabiensis  samples. Results PCR confirmed that  An. arabiensis  was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant F ST  was observed between all pairwise analyses of  An. arabiensis  populations. The Kassala state population indicated high genetic differentiation (F ST  ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the  An. arabiensis  populations investigated in Sudan, with the exception of Kassala state.

Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan