To better understand the phylogeography of Rhagoletis flies in the cingulata species group, we conducted a seven year host plant survey in México, behavioral observations, and studies on the basic biology of these tephritids. The survey revealed the existence of two geographically isolated Rhagoletis cingulata (Loew) populations in México. The first population was found to be restricted to Prunus serotina ssp. capuli (Cav.) McVaugh in an area within the central dry Altiplano spanning from Tlaxcala to México City and neighboring parts of the States of México, Puebla, and Hidalgo. The second population was found to infest Prunus serotina ssp. virens (Wooton & Standl.) McVaugh in high elevation areas of northeastern México between San Luis Potosí and Coahuila along the Sierra Madre Oriental. Both populations were hosts to the parasitoid Diachasmimorpha mellea (Gahan) (Hymenoptera: Braconidae), with percentage parasitism varying across sites. Collections of P. s. ssp. capuli and Prunus serotina Ehrh. ssp. serotina across the Eje Volcanico Trans Mexicano, the Sierra Madre del Sur, the Sierra de los Altos de Chiapas and mesic areas of the Sierra Madre Oriental between Veracruz and Queretaro failed to yield any pupae. Sites where pupae were recovered were significantly dryer than sites where R. cingulata was not found. Recovered flies were found to be univoltine and to overwinter as pupae. Adults in the field in Tlaxcala (Central Altiplano) were mainly sighted guarding, mating, and ovipositing in green fruit. Larval yield of fruit collected outside the natural area of distribution, and exposed to flies in the laboratory, was significantly lower than that of fruit collected within the natural range of R. cingulata. We compare distribution patterns with those of other species in the genus and discuss hypotheses to explain the outcome.