Pulmonary arterial hypertension (PAH) is a chronic disorder of the small pulmonary arteries, and the efficacy of the therapies and the prognosis remain poor. The pathobiology of PAH is complex, and needs to be elucidated by multiple approaches. The present study used a monocrotaline‑induced PAH rat model to perform a comprehensive microRNA (miRNA) microarray screening in the lungs and identified 16 downregulated miRNAs in the lungs from PAH rats. High‑enrichment gene ontology (GO) analysis identified several sets of genes, and established the miRNA‑mRNA network by outlining the interactions of miRNA and GO‑associated genes. Three downregulated miRNAs [miRNA 125‑3p (miR‑125‑3p), miR‑148‑3p and miR‑193] displayed the most marked regulatory function, and miR‑148‑3p and miR‑193 were observed to have the highest number of target mRNAs. Signaling pathway analysis demonstrated 26 signal transduction pathways, with MAPK, TGF‑β and cell cycle signaling as the most prominent. In addition, 342 genes were identified as the potential targets of these 16 miRNAs. Thus, a set of miRNAs in the lungs from rats with PAH and novel associations between biological events and PAH pathogenesis were identified, providing potential therapeutic targets for this disorder.