The frequency of harmful algal blooms (HABs) has increased over the last two decades, a phenomenon enhanced by global climate change. However, the effects of climate change will not be distributed equally, and Chile has emerged as one important, vulnerable area. The Chilean Patagonian region (41‒56°S) hosts two marine ecoregions that support robust blue economies via wild fisheries, aquaculture, and tourism. However, the harmful algal bloom-forming dinoflagellate Alexandrium catenella, a causative agent of paralytic shellfish poisoning outbreaks, threatens the viability of blue industries in this region and others worldwide. Despite the proliferation of A. catenella blooms over the last few decades, the role of sedimentary resting cysts in the recurrence of harmful algal blooms and the species' northward expansion across Chilean Patagonia is not well understood. As a resting cyst-producing species, the sediment-cyst dynamics of A. catenella likely contribute to the geographical expansion and bloom recurrence of this species. For this purpose, we analyzed a decade of A. catenella surface sediment cyst records across the two ecoregions of the Chilean Patagonian System that were further stratified into five subregions based on water temperature, salinity, dissolved oxygen, and nutrient characteristics. We also analyzed spatio-temporal cyst dynamics in a pre-, during-, and post-bloom scenario of the Chiloense ecoregion (more northern) of the Magellanic province. Our results indicated highly variable A. catenella resting cyst abundances, with a maximum of 221 cysts cm-3 recorded in 2002 after an intense bloom. Generalized linear mixed models and linear mixed models found that sampling season, subregion, and Total Organic Matter (%) explained resting cyst presence and density. The results also demonstrated the presence of A. catenella cysts in northern subregions, evidencing the northward geographical expansion observed during the last few decades. The risks of A. catenella bloom recurrence from small, patchy resting cyst distributions across broad geographical areas and under changing environmental conditions are discussed.