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The availability of bacterial artificial chromosome (BAC) offers a good genomic platform for a targeted integration of an exogenous gene by a homologous recombination system in Escherichia coli. In combination with microinjection technology, this system allows for the analysis of various aspects of biological phenomena occurring in vivo using Japanese medaka fish (Oryzias latipes). Here we describe a streamlined procedure for selecting BAC clones based on the medaka University of Tokyo genome browser (UTGB), followed by rapid modification with enhanced green fluorescent protein (EGFP) or DsRed fragments for transgenic analysis in medaka. Experimental procedures for BAC DNA preparation, microinjection of medaka embryos and screening of resulting transgenic medaka carrying EGFP/DsRed modified BAC clones are also described.