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Wheat rusts, the dreadful fungal diseases caused by members of the Puccinia genus remain as a major threat to global wheat production and food security. The R-gene mediated resistance has been employed as an efficient approach to develop rust resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel genomics assisted molecular players, including non-coding RNAs for rust disease management. MicroRNAs are crucial regulators of genes associated with plant growth, development, abiotic and biotic stress responses. In this study, high throughput small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem rust and leaf rust, together with mock inoculated controls. While miRNA mining in stem rust inoculated libraries revealed a total of twenty-six known and seven novel miRNAs, the search in leaf rust libraries culminated with twenty-two known and four novel miRNAs. The identified candidate miRNAs constituted both guide and passenger miRNA strands along with their isomiRs. Temporal expression pattern of differentially expressed miRNAs pinpoints their possible role during the progress of infection. Comparative analysis provides a better understanding of altered miRNA profiles associated with Sr36 and Lr45 disease resistance genes in response to stem rust and leaf rust, respectively. Also, the disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 with various sub-genomal origins might serve as an important common link between stem rust and leaf rust defense mechanisms downstream to the respective R-genes. Further, cis-regulatory elements that modulate MIR genes, targets of identified miRNAs related to various signal transduction pathways, and miR-SSRs which might be useful for rust disease control, are the emphasized attributes of our results. The outcome from this simultaneous study of miRNA profiles among two rust diseases and further characterization of the identified miRNAs can contribute to the expanding rust disease management programs.