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<p>Abstract</p> <p>Background</p> <p>The fibrinogen-like (FBG) domain consists of approximately 200 amino acid residues, which has high sequence similarity to the C-terminal halves of fibrinogen β and γ chains. Fibrinogen-related proteins (FREPs) containing one or more FBG domains are found universally in vertebrates and invertebrates. In invertebrates, FREPs are involved in immune responses and other aspects of physiology. To understand the complexity of this gene family in <it>Drosophila</it>, we analyzed FREPs in twelve <it>Drosophila </it>species.</p> <p>Results</p> <p>Using the genome data from 12 <it>Drosophila </it>species, we identified FBG domains in each species. The results show that the gene numbers in each species vary from 14 genes up to 43 genes. Using sequence profile analysis, we found that FBG domains have high sequence similarity and are highly conserved throughout. By comparison of structure and sequence conservation, some of the FBG domains in <it>Drosophila melanogaster </it>are predicted to function in recognition of carbohydrates and their derivatives on the surface of microorganisms in innate immunity.</p> <p>Conclusion</p> <p>Sequence and structural analyses show that FREP family across 12 <it>Drosophila </it>species contains conserved FBG domains. Expansion of the FREP families in <it>Drosophila </it>is mainly accounted by a major expansion of FBG domains.</p>