The Mexican fruit fly, Anastrepha ludens Loew, is a significant pest in mango and citrus production areas of Mexico. In this study, we evaluated the effects of some geographic characteristics, rainfall period, soil micro-environmental, and soil coverage variables on the occurrence of entomopathogenic fungi (EPF) associated with A. ludens larvae in soils of mango, grapefruit and mixed crops in central Veracruz state, Mexico. EPF isolates were characterized morphologically and identified by sequence analysis of elongation factor (EF1-1018F, EF1-1620R). We recorded four species of EPF (Metarhizium robertsii J.F. Bisch, S.A. Rehner & Humber [Hypocreales: Cordycipitaceae], M. brunneum Petch [Hypocreales: Cordycipitaceae], M. pinghaense Q.T. Chen & H.L. Guo [Hypocreales: Cordycipitaceae], and Beauveria bassiana (Balsamo) Vuillemin [Hypocreales: Cordycipitaceae]), of which Metarhizium robertsii was the most abundant and the most virulent. Also, we found that rainfall period, organic matter, coverage of herbs and forbs, and calcium levels modulated EPF occurrence. We estimated lethal concentrations for A. ludens larvae of the four most promising isolates, V3-123, V3-160, V1-332, and V3-369. Our results suggest that M. robertsii obtained from agricultural soils holds potential as a biological control agent for A. ludens.