Winnowing of poorly-adapted species from local communities causes shifts/declines in species richness, making ecosystems increasingly ecologically depauperate. Low diversity can be associated with marginality of environments, which is increasing as climate change impacts ecosystems globally. This paper demonstrates the demographic mechanisms (size-specific mortality, growth, fertility; and metapopulation connectivity) associated with population-level changes due to thermal stress extremes for five zooxanthellate reef-coral species. Effects vary among species, leading to predictable changes in population size and, consequently, community structure. The Persian/Arabian Gulf (PAG) is an ecologically marginal reef environment with a subset of Indo-Pacific species, plus endemics. Local heating correlates with changes in coral population dynamics and community structure. Recent population dynamics of PAG corals were quantified in two phases (medium disturbed MD 1998-2010, severely disturbed SD 1996/8, 2010 with two stable states of declining coral frequency and cover. The strongest changes in life-dynamics, as expressed by transition matrices solved for MD and SD periods were in Acropora downingi and Porites harrisoni, which showed significant partial and whole-colony mortality (termed "shrinkers"). But in Dipsastrea pallida, Platygyra daedalea, Cyphastraea microphthalma the changes to life dynamics were more subtle, with only partial tissue mortality (termed "persisters"). Metapopulation models suggested recovery predominantly in species experiencing partial rather than whole-colony mortality. Increased frequency of disturbance caused progressive reduction in coral size, cover, and population fecundity. Also, the greater the frequency of disturbance, the more larval connectivity is required to maintain the metapopulation. An oceanographic model revealed important local larval retention and connectivity primarily between adjacent populations, suggesting that correlated disturbances across populations will lead to winnowing of species due to colony, tissue, and fertility losses, with resultant insufficient dispersal potential to make up for losses-especially if disturbances increase under climate change. Variable extinction Riegl et al. Coral Winnowing in PAG Reefs thresholds exist based on the susceptibility of species to disturbance ("shrinkers" vs. "persisters"), determining which species will be winnowed from the community. Besides projected changes in coral community and population structure, no species are projected to increase in cover. Increased marginality due to climate change will lead to a net loss of coral cover and novel communities in PAG.