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The red macroalga <i>Gracilaria vermiculophylla</i> invasion provides an opportunity to investigate the evolution of biphasic life cycles and of reproductive modes by understanding how they structure and contribute colonizing new environments in natural conditions. In hard bottom habitats, we find gametophytes and tetrasporophytes fixed by holdfasts to hard substrates, whereas in soft bottom habitats, we find free-living tetrasporophytes either drifting or anchored by tube-building polychaetes. We collected thalli from hard and soft bottom habitats along the Eastern Shore of Virginia and Maryland to investigate the role of substrate on life cycle and reproductive mode dynamics. We determined the phase and sex using observable reproductive structures and a sex-linked PCR assay, followed by genotyping all thalli using nine microsatellite loci. Sexual reproduction prevailed in hard bottom sites, whereas clonal (asexual) reproduction dominated soft bottom sites and was accompanied by tetrasporophytic dominance. There was site-specific variation in selfing and clonal rates that are supported by observations of physiological stress and local extirpation, such as at Ape Hole Creek and Fowling Point, respectively. We found evidence of isolation by distance and the structuring of genetic diversity by habitat type, then site, and finally by year. While broad patterns have been described across the extant range, we clarify population genetic patterns in hard versus soft bottom habitats that are not confounded by the invasion history comparing native and non-native thalli. These results have implications for the on-going spread of this alga and contribute to our understanding of the population genetics of partially clonal taxa.