The elimination of lower trophic levels following severe habitat disturbance can trigger new community assembly processes. However, little is known about how past habitat disturbances have affected codependent evolution of trophically-linked and closely interacting taxa. Using genome-wide analysis of a macroalgal community affected by ancient catastrophic coastal uplift, we track the ecological dynamics of past co-dispersal and co-diversification among obligate interacting taxa. Our study reveals rapid and concerted reassembly of an intertidal community following disturbance. Specifically, hierarchical co-demographic analyses of multispecies genomic data support synchronous expansions of four strictly intertidal species in the wake of tectonic disturbance. These data show that tight algal-epifaunal links underpin parallel demographic responses across distinct trophic levels. These results highlight that high-resolution comparative genomic data can elucidate the strength of obligate ecological interactions, and the evolutionary dynamics of past co-dispersal and co-diversification in post-disturbance communities.