Mass mortality events (MMEs) are increasing globally in frequency and magnitude, largely due to human-induced change. The effects of these MMEs, both in the long- and short-term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with MMEs. Here, we use reduced-representation sequencing to identify potential short-term genetic impacts of an MME associated with a sea star wasting (SSW) outbreak. We tested for changes in the population for genetic differentiation, diversity, and effective population size between pre-SSW versus post-SSW populations of Pisaster ochraceus — a species that suffered high SSW-associated mortality (75–100% at 80% of sites). We detected no significant population-based genetic differentiation over the spatial scale sampled, however, the post-SSW population tended toward more differentiation across sites than the pre-SSW population. Genetic estimates of effective population size (N_e) did not detectably change, consistent with theoretical expectations; however, rare alleles were lost. While we were unable to detect significant population-based genetic differentiation or changes in N_e over this short time period, the genetic burden of this MME may be borne by future generations, unless widespread recruitment mitigates the population decline. Prior results from P. ochraceus indicated natural selection played a role in altering allele frequencies following this MME. In addition to the role of selection found in a previous study on the genomic impacts of SSW on P. ochraceus, our current study highlights the potential role the stochastic loss of many individuals plays in altering how genetic variation is structured across the landscape. Future genetic monitoring is needed to determine long-term genetic impacts in this long-lived species. Given the increased frequency of MMEs, it is important to implement demographic and genetic monitoring strategies that capture baselines and background dynamics to better contextualize species’ responses to large perturbations.

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