Subtropical reefs host a dynamic mix of tropical, subtropical, and temperate species that is changing due to shifts in the abundance and distribution of species in response to ocean warming. In these transitional communities, biogeographic affinity is expected to predict changes in species composition, with projected increases of tropical species and declines in cool-affinity temperate species. Understanding population dynamics of species along biogeographic transition zones is critical, especially for habitat engineers such as sea urchins. We investigated the population dynamics of sea urchins on coral-associated subtropical reefs at 7 sites in eastern Australia (28.196°S to 30.95°S) over 10 years (2010 – 2019). Counter to expectation, biogeographic affinity did not explain shifts in species abundances in this region. Although we expected the abundance of tropical species to increase at their cold range boundaries, tropical Diadema species declined across all sites. The subtropical T. australiae also showed decadal declines, while populations of the temperate C. rodgersii were remarkably stable throughout our study period. Our results show that temporal patterns of sea urchin populations in this region cannot be predicted by bio-geographic affinity alone and contribute critical information about the population dynamics of these important herbivores along this biogeographic transition zone.