Phylogenies can provide valuable information on biotic and abiotic factors associated with speciation. We examined species relationships in Tristerix (Loranthaceae), a genus of 11 species with an Andean distribution from Colombia to Chile. A previous classification divided Tristerix into subgenera Tristerix (two species) and Metastachys (nine species). We tested this classification by generating a molecular phylogeny of the genus using nuclear ribosomal DNA ITS and chloroplast atpB-rbcL intergenic spacer and trnL-F regions. All partitions generally gave congruent trees, thus a combined analysis was conducted. Tristerix was composed of a northern clade (six species) and a southern clade (four species). Tristerix verticillatus and T. penduliflorus (Metastachys) were strongly supported as members of the (southern) subgenus Tristerix clade. Speciation appears to be correlated with the emergence of matorral and cloud forest biomes and is driven by interactions with pollinators and seed dispersers. Tristerix aphyllus is sister to T. corymbosus of the matorral, not to neighboring temperate forest populations, thus rendering the latter species paraphyletic. This ecological speciation event may have occurred in sympatry. Tristerix provides excellent examples of how, during the orography of the Andes, many dynamic and interacting ecological factors have influenced their speciation.