Molecular markers have a high potential to resolve genetic differentiation within species and populations in the pelagic realm where barriers to gene flow cannot be easily identified. In the present study Calanoides carinatus (Copepoda, Calanoida), an ecologically important compo- nent of African upwelling systems, was investigated aiming to (1) describe spatial patterns in the distribution of genetic variance, (2) identify potential barriers that may have shaped the ge- netic structure of the species and (3) look for cryptic species. Samples were obtained in the eastern Atlantic Ocean from the Iberian Peninsula to Namibia. Analysis of mitochondrial (cy- tochrome oxidase c subunit I; COI) and nuclear (citrate synthase; CS) marker genes revealed a genetically-cohesive population of C. carinatus along the west coast of Africa. Haplotype sharing of C. carinatus populations, relatively few private alleles and a prevalent shift in allele frequencies indicated ongoing gene flow within the study area. Significant genetic differentia- tion of C. carinatus populations was discovered between the northern and southern hemisphere which may point to a potential, but permeable barrier close to the equator, possibly triggered by discontinuity of ocean currents in the equatorial region. No vertical genetic structuring in C. car- inatus was observed among the active surface population and deep-living resting stages in the northern Benguela indicating that horizontal differentiation was more pronounced than vertical structuring of populations. The occurrence of three diverse sequences of mitochondrial COI and their absence within nuclear CS, rather suggests marker evolution of COI than a cryptic species.