Relevant dataset associated with the PhD chapter "Integrating multiple species connectivity and habitat quality into conservation planning for coral reefs”. Data was compiled from previous chapters and additional data on biodiversity. Data on biodiversity includes: (i) spatial data representing coral reef ecosystems derived from satellite imagery; (ii) species distribution data for 405 species of reef fish from a geographic range data set compiled by a previous study (Vila-Nova et al. 2014; see thesis for the full reference). Data on connectivity and climate warming were collected as previously described in other chapters. All Brazilian reefs were used for this study. Data was collected to demonstrate how functional demographic connectivity for four candidate reef-associated species with varying dispersal abilities and a suite of connectivity metrics weighted by habitat quality can be used to set conservation objectives and inform marine protected area placement. Data was collected to explore interactions between different sets of objectives (i.e. biodiversity, connectivity, and climate warming) and evaluate the consequences of pursuing single objectives in marine planning.