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Throughout the Galápagos, differences in coral reef development and coral population dynamics were evaluated by monitoring populations from 2000–2019, and environmental parameters (sea temperatures, pH, NO₃⁻, PO₄³⁻) from 2015–19. The chief goal was to explain apparent coral community differences between the northern (Darwin and Wolf) and southern (Sta. Cruz, Fernandina, San Cristóbal, Española, Isabela) islands. Site coral species richness was highest at Darwin and Wolf. In the three most common coral taxa, a declining North (N)-South (S) trend in colony sizes existed forPorites lobataandPocilloporaspp., but not forPavona  spp. Frequent coral recruitment was observed in all areas. Algal competition was highest at Darwin, but competition by bioeroding sea urchins and burrowing fauna (polychaete worms, bivalve mollusks) increased from N to S with declining coral skeletal density. A biophysical model suggested strong connectivity among southern islands with weaker connectivity to Wolf and even less to Darwin. Also, strong connectivity was observed between Darwin and Wolf, but from there only intermittently to the south. From prevailing ocean current trajectories, coral larvae from Darwin and Wolf drift primarily towards Malpelo and Cocos Islands, some reaching Costa Rica and Colombia. Mean temperature, pH, and PO₄³⁻declined from N to S. Strong thermocline shoaling, especially inmore »the warm season, was observed at most sites. A single environmental factor could not explain the variability in observed coral community characteristics, with minimum temperature, pH and nutrient levels the strongest determinants. Thus, complex environmental determinants combined with larval connectivity patterns may explain why the northern Galápagos Islands (Darwin, Wolf) have higher coral richness and cover and also recover more rapidly than central/southern islands after region-wide disturbances. These northern islands are therefore potentially of critical conservation importance as important reservoirs of regional coral biodiversity and source of larvae.