In northern Tamaulipas, México, the contamination of corn by toxigenic fungi reduces grain production and quality. Corn contaminated by mycotoxins puts humans and livestock at risk. Continuous monitoring of the sanitary quality of grain at harvest and in storage will define preventive and corrective strategies for contamination by mycotoxigenic fungi. In this work, we identified toxigenic fungi associated with corn grown and stored in northern Tamaulipas, identified and quantified aflatoxins and their relationships with the physicochemical characteristics of the grain, and identified the main genes responsible for aflatoxin production in A. flavus. Fungal incidence was evaluated in vitro, aflatoxin production was evaluated via HPLC, and physicochemical traits were evaluated via spectrophotometry. Three genera were identified: Fusarium, Aspergillus, and Penicillium; the latter had the highest incidence in both 2011 and 2012. The incidence was higher in 2012 (82.3%) than in 2011 (4.5%), and storage did not affect the incidence. Associations among fungal incidences and physicochemical traits were significant and intermediate in both years. AFB1 production was negatively associated with hectoliter weight, and total fungal incidence was positively related to the incidence of Penicillium, Fusarium, and Aspergillus and negatively related to the flotation index. AFB1 was detected in 13.18% of the samples, with values ranging from 3.4881.33 ppb upon receipt and from 4.3245.92 ppb after storage. Two samples exceeded the allowed limits for Mexico (20 ppb). The aflD and aflQ genes were detected in 52.1 and 56.3%, respectively, of the A. flavus isolates.