Abstract Monarch butterflies, Danaus plexippus (L.), from eastern North America are well known for their incredible autumn migration to Mexico; however, not all monarchs follow this route. There is evidence of monarchs overwintering and reproducing in Florida, arriving to insular and continental Caribbean, and roosting by the thousands in the Yucatán, Mexico. This work aims to present evidence that these monarchs are part of two current migratory routes, that we consider as the south-eastern and the Atlantic routes, routes that were probably more prominent in the past. Monarchs were collected for 12 months in south Florida, for 4 years in Cuba in November and once in March, in the Yucatán and Guatemala at different times, and once in northern Venezuela. We used two independent techniques, stable hydrogen isotope (δ2H) analyses of the wings and/or thin layer chromatography (TLC), to trace the monarch’s natal grounds. We analysed the DNA of monarchs collected in St. Marks in the Florida Panhandle, Cuba and Guatemala, and compared those data against previously-analysed DNA data from monarchs in the Americas to characterize their genetic structure and to assess the possible movement and presence of North American monarchs and/or their alleles outside the USA. Our results support the existence of south-eastern and Atlantic migratory routes. TLC, isotope and DNA analyses showed the arrival of likely North American monarchs in Cuba, Yucatán, Guatemala, Venezuela and other areas of the Americas. North American monarchs found in these areas have different natal grounds, phenotypic traits and DNA signature than Mexican migrants. Monarchs from the south-eastern route mostly originated in the south-east USA and fed on local Asclepias spp., such as Asclepias viridis, Asclepias humistrata, Asclepias perennis and Asclepias asperula. Butterflies from this migratory route move east, enter the Florida Peninsula, pass to Cuba, fly to the Yucatán and then to Guatemala where they appear to overwinter in the high mountains of Guatemala where Abies guatemalensis occurs. Monarchs that are part of the Atlantic route move east of the Appalachians, enter the Florida Peninsula, and from there pass to the insular and continental Caribbean. The main host plants for the Atlantic monarchs are A. perennis and A. humistrata; in contrast, Mexican monarchs mainly feed on Asclepias syriaca. Some monarchs from these two proposed migratory routes, south-eastern and Atlantic, will stay in the places where they travelled and others will return via Florida and Mexico. We propose a scenario for how the different migratory routes evolved.