Value of the Data •Streptomyces sp. SS52 isolated from Phyllathus urinaria can produce daidzein, the isoflavone having several important biological activities. •The genome sequence data of Streptomyces sp. SS52 will be useful for the experimental identification of genes involved in the biosynthesis of daidzein. •In Streptomyces sp. SS52 genome, 7 putative genes involved in biosynthesis of daidzein were identified. •Data presented here could contribute to clarify the molecular mechanism of daidzein biosynthesis which is now poorly understood in Streptomyces bacteria.