Based on the superposition of 19 individual tracks of American species of the freshwater copepod genus Eucyclops, two generalized tracks were found. The Western Amazonian track (southern Peru, eastern Brazil, and central Colombia) corresponding to the Amazonian subregion and the South American Transition Zone, and the Mesoamerican-Northwestern South American track (central Colombia, Central America, and northeastern Mexico) corresponding to the Neotropical region, the Mexican Transition Zone, and the Nearctic region. One node was found in Colombia, an area where both generalized tracks intersect. The distributional patterns of Eucyclops apparently involve two cenocrons: one Holarctic, and another Paleotropical. The Western Amazonian generalized track can be correlated with the existence of rivers that function either as barriers or dispersal passageways, the uplift of the Andes, and the presence of the Miocene “Pebas lake/wetland system.” The Mesoamerican-Northwestern South American generalized track can be associated with climate changes resulting from the uplift of North American mountain ranges, the presence of marine barriers (Isthmus of Tehuantepec and Panama) and the uplift of mountains in southern Mexico and Central America. The closing of the marine barrier represented by the Isthmus of Panama seems to have been a key event in the northward and southward dispersal of Eucyclops in the Americas.