The bacterial phage ΦBT1 integrase is a promising tool due to its site-specific transgene character. It enriches the site-specific transgenic tools and provides the possibility for multiple site-specific transgenic manipulations. To improve its safety as a vector of gene therapy, it is necessary to investigate the potential interactions between ΦBT1 and proteins in mammalian host cells. Yeast mating and co-immunoprecipitation assay indicated that a tetrapeptide 433RFAL436 in ΦBT1 integrase was responsible for ΦBT1 and Daxx interaction. It was also demonstrated that over-expression of Daxx could reduce ΦBT1 mediated recombination rate in 293T cells by using ΦBT1 report system. It is the first time to identify a cellular protein interacting with ΦBT1 integrase and inhibiting its recombination efficiency. This result might be useful for improving the ΦBT1 integrase mediated transgene methods and directing the selection of target cells for ΦBT1 integrase.