Three new species of Micrura are described from shallow water of the Belize barrier reef and Bahia Almirante, Panama. Specimens were found at 0-30 m depth in association with a variety of rubble and its encrusting epibiota. The three species are morphologically very similar to each other, and are distinguished here primarily by color and by substantial differences in nucleotide sequence data for 16S rDNA and 28S rDNA. As many Micrura, they are slightly compressed dorso-ventrally, possess a caudal cirrus, and the cephalic lobe is bluntly rounded anteriorly and is the same width as the body. At least one species has distinct oblique musculature between the body-wall circular and inner longitudinal musculatures. One of the three species possesses a new morphotype larva rather than the expected typical pilidium larva.