Climate change has been hypothesized as a driver of recent increases in the prevalence and impacts of coral diseases. Little is known about the mechanism through which environmental stressors like temperature influence host resistance and overall disease dynamics. In this study we examined biochemical and cellular immune parameters in two species of coral during a naturally occurring temperature anomaly. In the summer and fall of 2005 water temperatures in the Caribbean were the highest levels recorded in the last century and resulted in a major coral bleaching event with subsequent disease outbreaks. Using corals collected from field sites in Puerto Rico and the Florida Keys we evaluated the effects of this climate anomaly on coral immunity and disease dynamics. Activities of known immune proteins such as prophenoloxidase, lysozyme and anti-bacterial activity were monitored in the reef building coral Montastraea faveolata. As a measure of cellular immunity, amoebocyte concentrations were monitored in the gorgonian coral Gorgonia ventalina. In this paper we present data demonstrating that some components of immunity respond to natural temperature stress as predicted and are suppressed, while others are actually activated by elevated temperatures, suggesting a general stress response or resilience to a changing environment.