We collected the ostracod Alternochelata lizardensis Kornicker 1982 via sediment sampling and evening plankton tows at Lizard Island, Queensland, Australia. While only previously described from samples that lost their natural color, we report males of the species to have bright green bundles of pigment throughout the inner carapace membrane and at specific locations on the ostracod’s body and an unusually colorless and translucent carapace. Females have a heavier carapace and some green pigmentation. We found, in a morphological phylogenetic analysis of Rutidermatidae, that A. lizardensis is part of a paraphyletic grade with other species of Alternochelata Kornicker, 1958 and Scleraner Kornicker, 1975. The analysis also supports a monophyletic Rutiderma Brady \& Norman, 1896. We also explored with microscopic and bioinformatic techniques the nature of the unusual green coloration of A. lizardensis and tested the hypothesis that it harbors photosynthetic symbionts. We first sequenced RNA extracted from the entire body of females and searched for genetic markers of possible photobionts. We found genetic matches for two species of cyanobacteria commonly found in seawater. Using fluorescent confocal microscopy to search for chlorophyll autofluorescence in the green patches, we nevertheless found no evidence for the presence of chlorophyll. From these analyses, we concluded there is no evidence that A. lizardensis harbors photosynthetic symbionts suggesting the green coloration is due to something besides photosynthetic symbionts. The framework we present here is nevertheless applicable for other taxa where photobionts are suspected.