MicroRNA (miRNA) molecules have a broad-spectrum effect due to their regulatory potential in almost all biological and metabolic processes including plant stress adaptation mechanism. Due to their high conservation, sequences of miRNA provide an effective type of putative functional markers which responsiveness may be species-, tissues/organs- and genotype-specific. Genomic characterization of 15 common oat genotypes of various origin was performed by several miRNA-based markers (miR156, miR398, miR399, miR408, miR827 and miR858). The marker miR408 showed the highest polymorphism and the highest amplification rate (almost 27% of all amplified loci). This type of miRNAs is part of the regulatory mechanisms of photosynthesis and processes related to biomass production. Markers related to nitrogen (miR827), phosphorus (miR399) and copper (miR398) metabolism together account for 47% of amplified miRNA loci. Markers related to flavonoid biosynthesis (miR156 and miR858) together account for 26%. In Sweden genotypes (Arne and Magne) was recorded the highest amplification of markers loci in general. MiRNA-based markers enabled screening of Avena sativa genomic polymorphism. By proteomics approaches (SDS and A-PAGE electrophoresis) was detected sufficient diversity between the analyzed samples, and genetic related dendrograms were constructed based on the electrophoretic profiles.