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The traditional camel breeding concept of pastoralists in the Nigeria-Niger corridor favours certain dromedary colour phenotypes, which are associated with distinct economic and behavioural traits. With the increasing requirement of sustainable food sources in desert environments the economic interest in Nigerian dromedaries has also been growing. In this study we used mitochondrial and microsatellite data to understand if the observed colour phenotypes correspond to genetically distinct groups and whether these groups reflect the breeding concept of camel pastoralists in the Nigeria-Niger corridor. Our results showed that Nigerian dromedaries are composed of a homogenous gene pool with no specific clustering according to coat colour. Significant but low nuclear and mitochondrial differentiation was detected only between dark-brown and black-brown camels. In addition to little evidence for population structure, Nigerian dromedaries exhibited a high genetic diversity, which could be explained by continuous gene flow with other populations during the annual transhumant voyage embarked upon by pastoralists on both sides of the Nigeria-Niger corridor. In comparison to local pastoralists’ knowledge, the molecular genetic data do not support a clear distinction into breeds (Ja, Kuril, and Kala) based on coat colour differences. (C) 2015 The Authors. Published by Elsevier B.V.