The term "Yoloxochitl" has historically been associated with Magnolia Mexicana (Magnoliaceae), a threatened species due to the decrease in its populations and areas where it thrives. The presence of two trees possibly of this species in Malinalco and Zumpahuacan, State of Mexico, raises questions about its history and scope of its distribution. The objective of the present study was to establish the existing molecular and morphological relationships between these individuals, with others of M. mexicana present in Zongolica, Veracruz. Samples of plant tissue were collected, and 18 morphological characters of trees from the municipalities of the State of Mexico, as well as M. mexicana, from Acontla and La Quinta in Zongolica Vercruz were determined. Also, as references of molecular contrast, samples of M. dealbata and M. grandiflora were used. 14 RAPD primers were analyzed, that amplified 205 bands, obtaining average PIC values of 0.30 and RP of 5.42, respectively. The cluster analysis formed three sets, two of them for the referents M. grandiflora and M. dealbata, and the third, grouped M. mexicana with the individuals of Malinalco and Zumpahuacan, sharing a genetic similarity of 87 and 90 % respectively. Morphological variation was also observed in 14 of 18 characters between individuals from Veracruz and those of the State of Mexico. The results indicated that the Yoloxochitl trees of Malinalco and Zumpahuacan belong to the Talauma section, however, they show a wide morphological variation with respect to M. mexicana.