Targeting genes involved in sexual determinism for vector or pest control purpose, requires a better understanding of their polymorphism in natural populations in order to ensure a rapid spread of the construct. By using genomic data from An. gambiae s.l., we analyzed the genetic variation and the conservation score of the fru gene in 18 natural populations across Africa. A total of 34339 SNPs were identified including 3.11% non-synonymous segregating sites. Overall, the nucleotide diversity was low and the Tajima's D neutrality test was negative indicating an excess of low frequency SNPs in the fru gene. The allelic frequencies of the non-synonymous SNPs were low (freq < 0.26) except two SNPs identified at high frequencies (freq > 0.8) in the Zinc-finger A and B protein domains. The conservation score was variable throughout the fru gene with maximum values in the exonic compared to the intronic regions. These results showed a low genetic variation in overall the exonic regions especially the male sex-specific exon and the BTB-exon 1 of the fru gene. These findings are crucial for the development of a gene drive construct targeting the fru gene that can rapidly spread without encountering resistance in wild populations.