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Honeybee populations in C&#244;te d&#8217;Ivoire have been previously identified as belonging to one subspecies, <i>Apis mellifera scutellata</i>, but other studies have since reported a mixed population consisting of <i>A. m. adansonii</i> and <i>A. m. jemenitica.</i> The population structure and the geographic distribution of honeybees in C&#244;te d&#8217;Ivoire remain unclear. This study aimed to profile the population structure of honeybees and their biogeography in C&#244;te d&#8217;Ivoire. A total of 33 honeybee colonies were sampled from 15 localities to investigate the maternal ancestry of indigenous honeybee populations using the DraI <i>COI</i>-<i>COII</i> mtDNA test. The results revealed that the honeybee population in C&#244;te d&#8217;Ivoire is composed of African haplotypes, all belonging to the A_I sublineage. Haplotypes A₁ and A₄ were recorded with five new sequence variants, including three types of haplotype A₁ and two types of haplotype A₄. The A_1e variant was the most frequent in the <i>A. m. adansonii</i> distributional area. The distribution of the haplotype variants was correlated with the climate pattern in C&#244;te d&#8217;Ivoire. This is the first study in C&#244;te d&#8217;Ivoire that gives insights into the biogeography and mitotype structure of the local honeybee populations.