Contracaecum bioccai n. sp. is described from the brown pelican Pelecanus occidentalis (L.) in northern Colombia (Totumo Marsh) based on 20 enzyme loci studied using multilocus allozyme electrophoresis. Moreover, genetic relationships between the new taxon and related congeners are presented based on allozyme data-sets and sequence analyses (519 bp) of the mtDNA-cox2 gene. Fixed allele differences were found at some of the allozyme loci analysed in comparison with other Contracaecum spp. from pelicans and cormorants [i.e. the sibling species of the C. rudolphii Hartwich, 1964 complex, C. septentrionale Kreis, 1955, C. micropapillatum (Stossich, 1890), C. microcephalum (Rudolphi, 1809) and C. pelagicum Johnston & Mawson, 1942]. The genetic distance, at the allozyme level, between C. bioccai n. sp. and its congeners ranged from D ( Nei ) = 0.80 versus C. septentrionale to D ( Nei ) = 1.40 versus C. micropapillatum. The genetic distance at the mtDNA cox-2 level ranged, on average, from K-2P = 0.12 versus the C. rudolphii species complex to K-2P = 0.15 versus C. micropapillatum. An overall concordant tree topology, obtained from UPGMA and NJ tree analyses inferred from allozyme data, as well as from MP, UPGMA and NJ inferred from mtDNA-cox2 sequence analysis, showed C. bioccai n. sp. as a separated lineage to the other Contracaecum spp. A concordant result was also obtained by PCA analysis based on both the allozyme and mtDNA cox-2 data-sets. All of the tree topologies, derived from the phylogenetic analysis inferred from both allozymes and mtDNA data-sets, were in substantial agreement and depicted C. bioccai as closely related to the sibling species of the C. rudolphii complex (C. rudolphii A and C. rudolphii B) and C. septentrionale. Morphological analysis and a differential diagnosis based on male specimens of C. bioccai, which had been genetically characterised by both allozyme markers and mtDNA sequences analysis with respect to morphologically related congeners, enabled the detection of differences in a numbers of characters, including spicule length, the morphology of the distal end of the spicule and the distribution patterns of the distal caudal papillae.