MicroRNAs (miRNAs) are 20-24 nucleotide long non-coding RNAs known to play important regulatory roles during plant development, organ morphogenesis, and stress responses by controlling gene expression. Although Vigna unguiculata (cowpea) is an economically important salt sensitive member of legumes, very little is known about the conserved miRNAs and their expression profile during salinity stress in this plant. In the present study using comparative genomic approach and following a set of strict filtering criteria we have identified 18 conserved V. unguiculata miRNAs belonging to 16 distinct miRNA families. Using these potential miRNA sequences 15 potential target genes were predicted and all of them were identified as transcription factors. Seven of these predicted V. unguiculata miRNAs were experimentally validated in the root tissues and found to be up-regulated during salt stress as revealed by quantitative real time PCR (qRT-PCR). Perfectly cleaved Auxin response factor (ARF), the target transcript of V. unguiculata miR160 was detected successfully by modified 5′ RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) method. © 2010 Springer Science+Business Media B.V.