The population of forest elephant has continuously declined in Côte d’Ivoire and, the remaining population largely consists of small populations that are fragmented and isolated. No data actually exist on the level of genetic diversity and population genetic structure of current forest elephant populations in Côte d’Ivoire need to be highlighted. In this sense, determining genetic diversity and the underlying mechanisms of population differentiation is crucial for the initiation of effective conservation management. Forest elephant dung samples were collected in three forest reserves (FR) in Côte d’Ivoire. The total genomic DNA was extracted from these samples, A total of 101 sequences of the mitochondrial DNA control region measuring 600 base pair and 31 haplotypes were obtained. A haplotypic diversity ranging from 0.655 ± 0.050 at Bossématié and 0.859 ± 0.088 at Port Gauthier was obtained. More than half (16 of 31) of the haplotypes observed were singletons and only the Dassioko and Port Gauthier FRs shared the same haplotypes. The strong genetic connectivity between forest elephant populations of the Dassioko and Port Gauthier FRs is supported by the grouping of these populations into a single cluster by Bayesian analysis and principal component analysis. Although populations of Loxodonta cyclotis still exhibit relatively high genetic diversity, habitat fragmentation has already affected the genetic variability of current populations. Urgent measures including the reinforcement/establishment of genetic corridors and the strengthening of protection measures need to be undertaken to save the remaining populations.