Corn is a main crop in Mexico, where 69 landraces are cultured by peasants in a non-synthetic crop improvement, obtaining seed-grain for autoconsumption. Corn agriculture has developed pathosystems in which phytopathogenic fungi, including Fusarium spp. could damage seeds on their physiological and food qualities due to mycotoxins contamination. Therefore, this study estimated the association between their incidence and 21 corn native populations from two states of Mexico: Mexico and Tlaxcala, in which five races were previously identified by morphometric characteristics. They were microbiologically analyzed, using the freeze blotter test with subsamples of 50 grains and four replications, from 10 ears, identifying and quantifying incidence of: Number of Phytopathogenic Fungi Genera (NPFG), Fusarium graminearum (FG) and Fusarium verticillioides (FV). Additionally, germination tests and ELISA (AgraQuant®, Romer-Labs.) tests were applied to detect contamination of Deoxynivalenol (DON), Zearalenones (ZON) and Fumonisins (FUM). Main Components (MCA) and Cluster Analysis (CA) estimated the association among those variables (Minitab, 16.0). CA generated seven groups of landraces revealing a differential incidence between FG (0- 31%) and FV (21.5-62.5 %) (r = - 0.225*). The NPFG were 2-8 genera biodiverse. MCA associated FV (32.17%), FG (22.33%), germination 74.3%, DON (1.640 ppm), ZON (0.330 ppm) and Cacahuacintle landrace in Mexico State; FV (50.13%), FG (9.5%), germination 93.5%, DON (0.400 ppm), ZON (0.000 ppm) and Cónico landrace in Tlaxcala. FUM was not detected.