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Introduction  Reef-building corals (Scleractinia) exhibit various colors, of which fluorescent proteins (FPs) are a major determinant. Gene duplication is considered a major mechanism in the generation of the  FP  gene family and color diversity. Examining gene duplication events and subsequent evolution may improve our understanding of  FP  gene family diversity.    Results  We isolated a novel  FP  gene family from one individual of  Montipora  sp., which we named  monGFP  ( GFP  gene from  Montipora  sp.). This gene family consists of at least four genes that produce at least six different cDNA sequences. The sequences were categorized into two types based on the length of cDNA; this difference is attributed to alternative splicing. Although the amino acid sequences were different, the emission spectra of the  monGFP  variants were nearly identical (518–521 nm). In addition to this gene family, we isolated ten paralogous  AdiFP10  ( Adi-Fluorescent protein-10  gene from  Acropora digitifera ) sequences from cDNA of two  Acropora  species,  A. digitifera  and  A. tenuis . Based on our phylogenetic analysis, five sequences from  A. digitifera  and four sequences from  A. tenuis  appeared to be in a different cluster from  AdiFP10 , suggesting a new  FP  gene cluster. The  FP  sequences were likely to have been generated independently in each species or generated by gene duplications in the ancestral lineage of  Acropora , followed by extensive gene conversion within each species.    Conclusion  Our results clarify a part of the diversification process of  FP  genes during the evolutionary history of  Montipora  and  Acropora  species. Our analyses of monGFP indicate that FPs translated from different splicing variants and gene copies have evolved without changes in the function of fluorescence, and gene copies have been evolved under purifying selection. On the other hand,  AdiFP10  paralogs and other  RFP  genes in  Acropora  species may have diversified their functions. Identification of conserved and divergent modes of evolution after the duplication of  FP  genes may reflect variation in the biological roles of different FPs.    Electronic supplementary material  The online version of this article (doi:10.1186/s40851-015-0020-5) contains supplementary material, which is available to authorized users.

Genetic diversity of fluorescent protein genes generated by gene duplication and alternative splicing in reef-building corals