Quantifying patterns of dispersal and settlement in marine benthic invertebrates is challenging, largely due the complexity of life history traits, small sizes of larvae (<1 mm), and potential for large-scale dispersal (>100 km) in the marine environment. Here, we develop a novel method that allows for immediate differentiation and visual tracking of large numbers of coral larvae (106 to 109) from dispersal to settlement. Neutral red and Nile blue stains were extremely effective in coloring larvae, with minimal impacts on survival and settlement following optimization of incubation times and stain concentrations. Field validation to wild-captured larvae from the Great Barrier Reef demonstrates the efficacy of staining across diverse taxa. The method provides a simple, rapid (<60 minutes), low-cost (approximately USD$1 per 105 larva) tool to color coral larvae that facilitates a wide range of de novo laboratory and field studies of larval behavior and ecology with potential applications for conservation planning and understanding patterns of connectivity.