Photosymbioses between animals and photosynthetic algae have independently evolved in diverse marine lineages from single-celled foraminiferans to complex organisms such as corals and bivalves. This amazing relationship lays foundation of coral reefs – one of the most diverse and productive ecosystem in the ocean. However, molecular mechanisms behind such symbioses remain less understood, especially for non-cnidarian organisms, such as mollusks. In order to fill this gap, we use the marine bivalve subfamily Fraginae (heart cockles), which establishes photosymbioses with algal lineages from the family Symbiodiniaceae, as a model system to identify photosymbioses-related genes. In this study, we assessed differential gene expression patterns in three photosymbiotic species (Fragum fragum, F. scruposum and F. sueziense), each kept under three different light intensities (normal, reduced, and dark). We obtained a total of 176 transcriptomes from both mantle (symbiont containing) and foot (no symbionts) tissues of the three bivalves through RNAseq. The genes whose expression patterns were highly regulated by light intensities, and are uniquely expressed in symbiont-containing tissues were identified as candidate photosymbiosis-related genes. Their functions in the photosymbiosis process were explored.