The paper describes a method for directly detecting DNA methylation without bisulfite conversion using single-molecule real-time (SMRT) sequencing. SMRT sequencing involves observing DNA polymerases catalyzing the incorporation of fluorescently labeled nucleotides into complementary strands. The arrival times and durations of fluorescence pulses provide information about polymerase kinetics, allowing direct detection of modified nucleotides such as N6-methyladenosine, 5-methylcytosine, and 5-hydroxymethylcytosine. The method leverages the intrinsic measurement of polymerase kinetics in SMRT sequencing, which does not affect the primary DNA sequence determination. The study demonstrates that different modifications affect polymerase kinetics differently, enabling discrimination between them. By combining circular consensus sequencing with principal component analysis, the method can achieve single-molecule identification of epigenetic modifications with base-pair resolution. This approach is suitable for long read lengths and can map methylation patterns within highly repetitive genomic regions. The technique is validated using synthetic DNA templates and a C. elegans fosmid from a *dam+* E. coli strain, showing that adenosine methylation alters polymerase kinetics in various sequence contexts.The paper describes a method for directly detecting DNA methylation without bisulfite conversion using single-molecule real-time (SMRT) sequencing. SMRT sequencing involves observing DNA polymerases catalyzing the incorporation of fluorescently labeled nucleotides into complementary strands. The arrival times and durations of fluorescence pulses provide information about polymerase kinetics, allowing direct detection of modified nucleotides such as N6-methyladenosine, 5-methylcytosine, and 5-hydroxymethylcytosine. The method leverages the intrinsic measurement of polymerase kinetics in SMRT sequencing, which does not affect the primary DNA sequence determination. The study demonstrates that different modifications affect polymerase kinetics differently, enabling discrimination between them. By combining circular consensus sequencing with principal component analysis, the method can achieve single-molecule identification of epigenetic modifications with base-pair resolution. This approach is suitable for long read lengths and can map methylation patterns within highly repetitive genomic regions. The technique is validated using synthetic DNA templates and a C. elegans fosmid from a *dam+* E. coli strain, showing that adenosine methylation alters polymerase kinetics in various sequence contexts.