Levels and origins of clonal diversity in asexual hybrid animals are critical to understanding how they can coexist with their sexual progenitor species. In this study, asexual gynogenetic hybrids between Fundulus diaphanus and Fundulus heteroclitus known from two sites in Nova Scotia (Canada) were characterized using discriminant morphological traits, eight microsatellite loci, and mitochondrial DNA. Fifteen clonal genotypes were uncovered, all bearing the same F. diaphanus maternal haplotye. Each site harboured a different dominant clone along with several rarer clones that all appear to be of recent origin. Unexpectedly, highly introgressed sexually reproducing hybrids (0.25 > q > 0.75) were also detected. Sexual hybrids with maternal ascendance in either species were also found at three other sites in the Atlantic region. Based on a single meristic trait (scale counts), it is shown that asexual clones can be significantly more variable than populations of sexual parental species. Also, species are morphologically more alike when living in sympatry, suggesting that introgression may occur via sexual hybrids. Altogether, these results confirm and refine the available knowledge on this hybrid system, and indicate that hybridization is probably a more widespread phenomenon than suspected, with implications for the phenotypic variability of a widely used model species, F. heteroclitus.