Metabolic syndrome (MS) is a proven risk factor for Breast Cancer (BCa). Previously, we found prominent epithelial lining in breast ducts of MS-like disease mice, obtained by chronically feeding animals with high fat diet (HFD). Our aim was to assess epigenetic alterations in breast ductal epithelium and tumors from HFD fed mice. H&E stains from breast tissues obtained from HFD fed Balb-c mice showed increased nuclei size and mitotic rate with presence of apoptotic bodies and nucleoli compared to control diet (CD) mice. Breast ductal epithelium from these mice were evaluated by immunohistochemistry (IHC) using antibodies against DNA methylation (5MC) and methylated histones (3MeH3-K4, -K9, -K27 and 2MeH3K36). We found no differences between groups by immunoreactive score. Nu/nu HFD or CD fed mice were inoculated with MDA-MB-231 cells. Xenografts showed no differences in methylated histones expression between groups, but HFD showed an increase of 5MC (IHC) and its enzyme DNMT1 (RT-qPCR) expressions. Analysis of multiple microarray datasets from patients (Oncomine) showed EZH2 and DNMT1 upregulated in BCa compared to normal breast tissue. Additionally, analysis of functional genomic datasets (UCSC Xena) revealed significantly increased (DNMT1, EZH2, SUV39H1, SUV39H2) or decreased (EZH1, SMYD1, SETD7) expression of methyltransferases in BCa tissue compared to normal tissue. We propose DNMT1 and EZH2 as potential biomarkers to further explore MS-associated BCa diagnosis.