Summary Objective To assess the role of imported cases in the local epidemiology of malaria and population genetics of Plasmodium falciparum in an urban endemic area in Colombia. Method A total of 679 P. falciparum cases presenting in the city were interviewed, mapped, and genotyped using msp1 and msp2 molecular markers. Results Among the cases, 75% were classified as imported and harboured single‐clone infections. The P. falciparum parasite population had low genetic diversity with a preponderant haplotype (mean genetic diversity H = 0.36), even when microsatellite markers were used ( H = 0.49), partly because of the small scale at which population movement was studied. Nevertheless, indigenous and potentially introduced cases were identified. Conclusion Migration is a confounder in planning malaria control in this endemic urban area. Longitudinal studies which monitor the P. falciparum population in imported and autochthonous cases at larger spatial scales would be necessary to study the effect of population movement on malaria transmission and, with suitable molecular markers, on the spread of drug resistance.