Coral fluorescence is attributed to genome-encoded fluorescent proteins (FPs). This fluorescence is proposed to contribute to coral colors. However, genetic bases of coral color are not well understood. Narrow band laser excitation measurements of live Acropora digitifera revealed a clear separation of fluorescence from reflectance, and showed a wide range of fluorescent emission. FP cDNA sequences from A. digitifera and A. tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into middle-wavelength emission (MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades. FP gene copy numbers in the genomes of four A. digitifera colonies were estimated as 16–22 in the MWE clade, 3–6 in the M/LWE clade, and 8–12 in the CP clade. Fluorescent light produced by recombinant protein products encoded by the newly isolated genes explained the fluorescent range of live A. digitifera, suggesting that coral fluorescence is determined by a multi-FP gene family. The functionally diverse multi-FP gene family must have existed in the Acropora species ancestor, suggested by phylogenetic analyses and evolutionary. Acropora species have persisted multi-FP gene family during their evolution.