We previously reported that the maintenance cytosine methyltransferase xDnmt1 is essential for gene silencing in early Xenopus laevis embryos. In the present study, we show that silencing is independent of its catalytic function and that xDnmt1 possesses an intrinsic transcription repression function. We show that reduction of xDnmt1p by morpholino (xDMO) injection prematurely activates gene expression without global changes in DNA methylation before the mid-blastula transition (MBT). Repression of xDnmt1p target genes can be reimposed in xDMO morphants with an mRNA encoding a catalytically inactive form of human DNMT1. Moreover, target gene promoter analysis indicates that silencing is not reliant on dynamic changes in DNA methylation. We demonstrate that xDnmt1 can suppress transcription activator function and can be specifically localised to non-methylated target promoters. These data imply that xDnmt1 has a major silencer role in early Xenopus development before the MBT as a direct transcription repressor protein.