A total of 20 plants belonging to different genera (Acalypha, Ageratum, Ambrosia, Bidens, Blechum, Caesalpinia, Calea, Carlowrightia, Croton, Eugenia (2), Furcraea, Stenandrium, Tephrosia, Trichilia (2), Randia (3), and Vitex) were selected from native flora of the Yucatan peninsula. All plants selected were collected and separated in to leaves, stems and roots. These were then extracted with ethanol and their crude extracts (54) were evaluated against Alternaria tagetica, Colletotrichum gloeosporioides, Fusarium oxysporum and Rhizopus sp. using the filter paper disc diffusion assay. Results lead to the selection of 33 crude extracts active against at least one of the target strains, which were assessed to determine their ability to inhibit the mycelial growth of the pathogenic fungi in a second antifungal assay. The results of this assay indicated that extracts from the roots of Croton chichenensis were the most promising, with a wide activity spectrum against all pathogens tested in both assays with inhibition percentages of greater than 60%. Furthermore, extracts from leaves of Ambrosia hispida, Trichilia minutiflora, and roots of Acalypha gaumeri were able to cause growth inhibition against two or three pathogen strains (≥50%). Studies of these active extracts should be continued at different levels. In general, results revealed a good bioactive potential of the flora from the Yucatan peninsula to produce metabolites with potential applications as botanical pesticides in the near future.