Role of cytosine methylation in Lr28-mediated leaf rust resistance in wheat was examined using MSAP and MeDIP. DNA digested with methylation sensitive restriction enzymes was used for MSAP, while 5’mC-immunoprecipitated DNA sequences were used for MeDIP. A pair of NILs i.e. susceptible cv. HD2329 and its resistant NIL HD2329+Lr28 were inoculated with virulent pathotype 77-5 of Puccinia triticina. DNA was isolated from the seedlings before inoculation (0hbi) and 96 hours after inoculation (hai) and utilized for MSAP and MeDIP. The data from MSAP and MeDIP together suggested both hypomethylation (activation) and hypermethylation (repression) for different genes in incompatible interaction, and large-scale hypomethylation (activation) in compatible interaction. Level of methylation and types of genes involved in methylation included the following. (i) Genes showing hypomethylation-mediated higher expression in incompatible interaction relative to compatible interaction (e.g., genes encoding ribosomal proteins S18/S16/L33/L16, NADH quinone oxidoreductase, glutathione S-transferase, glutaredoxin, ABC transporter, etc.). (ii) Genes showing hypermethylationmediated repression in resistant NIL (at 0 hbi) relative to susceptible NIL (at 0 hbi) that were later turned active due to hypomethylation in resistant NIL at 96 hai (e.g., NBS-LRR, terpine synthase, cellulose synthase, HSP70 etc.). (iii) Genes showing hypomethylation mediated activation during compatible interaction in susceptible NIL at 96 hai (e.g., acetyltransferase, citrate transporter, PR6, etc.). Level of methylation was generally abundant in intergenic regions followed by promoters, TTSs and exons/introns. Hypermethylation of the promoters was not always associated with inhibition of gene expression and vice-versa, indicating a complex relationship between methylation and gene expression, and suggesting involvement of other regulatory mechanisms. MSAP analysis also showed abundance of CmG methylation in compatible interaction and CmHG methylation in incompatible interaction, suggesting changes in methylation context also. The results of this study improved our understanding of the epigenetic control of leaf rust resistance in wheat. Future studies involving whole genome bisulfite sequencing using the same experimental material will supplement the above information