A drought tolerant cultivar of Pennisetum typhoides was chosen for the study and the seeds were subjected to 150mM salt and 15% PEG induced drought stress for 36h. 3 barcoded miRNASeq libraries were produced from leaf and root tissues, one from each treatment (control, drought and salt stressed). The leaf and root samples were pooled in equal concentration to reduce the number of libraries. All libraries were sequenced using Illumina HiSeq 2500 platform to generate 50bp single end reads. Quality of reads was assessed and improved using several tools. The reads from the Pennisetum sample was analyzed using miRDeep2 and psRNATarget to identify expressed miRNA (already annotated in miRBase) and novel miRNAs. Statistical analysis, including count normalization and differential expression was performed with edgeR using accession grouped leaf temperature, yield, condition (drought/salt stressed or control) and sample type (leaf or root) as factors. Differentially expressed microRNAs under abiotic stress conditions were analyzed further.