Resistant and susceptible interactions between nearly-isogenic melon (Cucumis melo) lines (Vat+ and Vat-) and cotton-melon aphids (Aphis gossypii) were examined to study the regulatory role of miRNAs in gene expression. Differentially regulated defense genes and transcription factors were identified by cDNA-AFLP and the expression profiles were confirmed by real-time PCR during early and late stages of aphid infestation. Several genes were implicated in the resistant response including beta 1,3 glucanase, receptor-like serine threonine kinase, XBAT35, MYB family of transcription factors, and BHLH family transcription factors. MicroRNAs, known to target these gene families, were identified from melon smallRNA libraries constructed from leaf tissues during early and late stages of A. gossypii infestation. MicroRNAs identified from melon smallRNAs libraries were confirmed by real-time PCR. The identification of defense genes, transcription factors and smallRNAs involved in the VAT-mediated resistance response will increase our understanding of both the specific mode of resistance and its regulation.