Knowledge of factors that influence species colonization and abundance during ecological succession is key for conservation and restoration efforts. The tolerance of species to environmental stresses and interspecific interactions influence stages of ecological succession. Species with high tolerance to stress or high competitive ability, such as invasive species or transgressive hybrids, may acquire a relevant role in the succession, inhibiting its development. We studied the role of native Sarcocornia and exotic Spartina hybrids on vegetation succession in salt marshes. In a time span of ca. 12 years, halophyte community structure and key sedimentary characteristics were recorded in marshes that differ in geomorphology, physiography, and successional status. We evaluated vegetation change in a young marsh undergoing rapid primary succession, and in a mature marsh undergoing slow changes in composition within established vegetation. Native hybrids increased their abundance in both types of marshes over time. Their presence and persistence was concurrent with colonization by other native halophytes. While they did not dominate the community and impede native succession, it is interesting to note their colonization coincided with a decrease in cover of invasive Spartina densiflora. In contrast, exotic hybrids formed from S. densiflora changed successional trajectories through competitive displacement of native halophytes in the mature marsh. However, these hybrids were not yet present in the young marsh where S. densiflora had just started to invade. This study reveals contrasting roles of invasive and native hybrids during ecological succession, providing valuable new knowledge for the management and conservation of salt marshes.