Summary: ipDMR is an R software tool for identification of differentially methylated regions (DMRs) using auto-correlated P-values for individual CpGs from epigenome-wide association analysis using array or bisulfite sequencing data. It summarizes P-values for adjacent CpGs, identifies association peaks and then extends peaks to find boundaries of DMRs. ipDMR uses BED format files as input and is easy to use. Simulations guided by real data found that ipDMR outperformed current available methods and provided slightly higher true positive rates and much lower false discovery rates. Availability and implementation: ipDMR is available at https://bioconductor.org/packages/release/bioc/html/ENmix.html. Supplementary information: Supplementary data are available at Bioinformatics online.