Active metabolites from plants are considered safer than synthetic chemicals for the control of plant-parasitic nematodes of the genus Meloidogyne. In the present work, 75 aqueous extracts (AEs) from different vegetative parts of 34 native plant species of the Yucatan Peninsula were evaluated against second-stage juveniles (J2s) of Meloidogyne incognita and M. javanica in microdilution assays. The highest mortality (M) against both Meloidogyne species was produced by the foliar AE from Alseis yucatanensis (M ≥ 94%) and Helicteres baruensis (M ≥ 77%) at 3% w/v after 72 h. Other active AEs at 3% were from the leaves of Croton itzaeus and stems of H. baruensis (M: 87–90%) on M. javanica and the stems of Annona primigenia and the leaves of Morella cerifera on M. incognita (M: 92–97%). The AEs from A. yucatanensis had the lowest LD50 against M. incognita (0.36% w/v), and against M. javanica (3.80% w/v). In an acute ecotoxicity assay of the most promising AEs using non-target earthworms (Eisenia fetida), the AE of A. yucatanensis had slight acute toxicity (LD50: 2.80% w/v), and the rest of the most active AEs were not ecotoxic. These tropical plants are potential candidates for further studies as biorational agents for controlling Meloidogyne species.