Fragmented forests often experience altered environmental conditions that can change species' behaviours and ranges, potentially leading to new hybridization opportunities. In some cases, hybridization can be beneficial, providing a genetic rescue effect for small, isolated populations by introducing new genetic material, increasing genetic diversity, and enhancing the population's ability to adapt to changing conditions. Conversely, hybridization can lead to outbreeding depression or even genetic swamping of parental species. Epidendrum orchids, a diverse genus in the neotropics, frequently hybridize in nature. Hybridization in this genus can be facilitated by their generalist pollination strategies, where multiple pollinator species visit the flowers. Natural hybrids among Epidendrum species have been observed in regions where their ranges overlap, with divergent evolutionary outcomes. In this study, we address if natural hybridization between two species of Epidendrum (E. calanthum and E. cochilidium) is more frequent in fragmented sites than in well-conserved forest patches. Morphometrics, plastid and AFLP markers, confirmed the presence of hybrids between the two species in seven out of eighteen samples. The hybrids exhibit a wide range of morphological traits including different colours, often blurring species discrimination. Undisturbed populations generally showed a lower number of hybrids, or only parental species. Establishing continuous monitoring of orchid populations and research on hybridization patterns would provide valuable insights into the dynamics of hybridization and inform conservation actions.