Cover crop species represent an affordable and effective weed control method in agroecosystems; nonetheless, the effect of its use on arbuscular mycorrhizal fungi (AMF) has been scantily studied. The goal of this study was to determine root colonization levels and AMF species richness in the rhizosphere of maize plants and weed species growing under different cover crop and weed control regimes in a long-term experiment. The treatment levels used were (1) cover of Mucuna deeringian (Muc), (2) "mulch" of Leucaena leucocephala (Leu), (3) "mulch" of Lysiloma latisiliquum (Lys), (4) herbicide (Her), (5) manual weeding (CD), (6) no weeding (SD), and (7) no maize and no weeding (B). A total of 18 species of AMF belonging to eight genera (Acaulospora, Ambispora, Claroideoglomus, Funneliformis, Glomus, Rhizophagus, Sclerocystis, and Scutellospora) were identified from trap cultures. Muc and Lys treatments had a positive impact on AMF species richness (11 and seven species, respectively), while Leu and B treatments on the other hand gave the lowest richness values (six species each). AMF colonization levels in roots of maize and weeds differed significantly between treatment levels. Overall, the use of cover crop species had a positive impact on AMF species richness as well as on the percentage of root colonized by AMF. These findings have important implications for the management of traditional agroecosystems and show that the use of cover crop species for weed control can result in a more diverse AMF community which should potentially increase crop production in the long run.