The outcome of natural hybridization is highly variable and depends on the nonexclusive effects of both pre- and post-mating reproductive barriers. The objective of this study was to address three specific questions regarding the dynamics of hybridization between the American and European eels (Anguilla rostrata and Anguilla anguilla). Using 373 AFLP loci, 1127 eels were genotyped, representing different life stages from both continents, as well as multiple Icelandic locations. We first evaluated the extent of hybridization and tested for the occurrence of hybrids beyond the first generation. Second, we tested whether hybrids were randomly distributed across continents and among Icelandic sampling sites. Third, we tested for a difference in the proportion of hybrids between glass eel and yellow eel stages in Iceland. Our results provided evidence for (i) an overall hybrid proportion of 15.5% in Iceland, with values ranging from 6.7% to 100% depending on life stages and locations; (ii) the existence of hybrids beyond the first generation; (iii) a nonrandom geographic distribution of hybrids in the North Atlantic; and (iv) a higher proportion of first and later generation hybrids in yellow eels compared to glass eels, as well as a significant latitudinal gradient in the proportion of hybrids in Icelandic freshwater. We propose that the combined effect of both differential survival of hybrids and variation in hybridization rate through time best explain these patterns. We discuss the possibility that climate change, which is impacting many environmental features in the North Atlantic, may have a determinant effect on the outcome of natural hybridization in Atlantic eels.