The Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulates gene expression, through predicting methylation sites of their promoters particularly in major crop species. In this study, we developed a user-friendly prediction server for accurate prediction of 6mA sites by incorporating a robust feature set, viz., Binary Encoding of Mono-nucleotide DNA. Our model,MethSemble-6mA, outperformed other state-of-the-art tools in terms of accuracy (93.12%). Furthermore, we investigated the pattern of probable 6mA sites at the upstream promoter regions of the LBD-containing genes in Triticum aestivum and its allied species using the developed tool. On average, each selected species had four 6mA sites, and it was found that with speciation and due course of evolution in wheat, the frequency of methylation have reduced, and a few sites remain conserved. This obviously cues gene birth and gene expression alteration through methylation over time in a species and reflects functional conservation throughout evolution. Since DNA methylation is a vital event in almost all plant developmental processes (e.g., genomic imprinting and gametogenesis) along with other life processes, our findings on epigenetic regulation of LBD-containing genes have dynamic implications in basic and applied research. Additionally, MethSemble-6mA (http://cabgrid.res.in:5799/) will serve as a useful resource for a plant breeders who are interested to pursue epigenetic-based crop improvement research.