In order to investigate cellular and molecular mechanisms involved in symbiosis of scleractinian corals with photosynthetic dinoflagellate algae using in vitro system, our previous studies have established approximately 15 cell-culture lines derived from planula larvae of Acropora tenuis. Based on cell their morphology and behavior, they were classified into three types, flattened amorphous cells (FACs), vacuolated adherent cells (VACs), and small smoothened cell (SSCs). Of them, FACs include fibroblast-like cells and neuroblast-like cells. Fibroblast-like cells were likely of endodermal origin, and when mixed with dinoflagellates, the cells incorporated algae in short time. On the other hand, the property of VACs and SSCs remains to be determined. This study compared differential expression profiles of genes using RNA-seq among the three types.