Background Pulmonary Arterial Hypertension (PAH) is a rare disease where the thickening of the precapillary pulmonary arteries ends up inducing right heart failure. Nowadays, obtaining an early diagnosis is challenging and typically delayed until undergoing right-heart catheterization. Methods We performed small RNA sequencing (microRNA-seq) in the plasma of idiopathic PAH patients and controls, that we validated by qPCR. We then interrogated the role of miR-3168 in HUVECs by performing western-blot, flow cytometry and tube formation assays. Results We found 29 differentially expressed microRNAs and validate 7 of them let-(7a-5p, let-7b-5p, let-7c-5p, let-7f-5p, miR-9-5p, miR-31-5p, miR-3168) in a nationwide cohort of 120 patients and 110 controls. We then used classification models to analyze their potential as PAH predictor. In the first half of our cohort, we obtained a model with an AUC of 0.888. Although, this value lowered to 0.738 after using this model in the whole cohort of patients. Additionally, we validated the effect of miR-3168, a novel upregulated miRNA in PAH patients which targets BMPR2, and impairs angiogenesis, as assessed by the tube formation assay. Conclusion We identified novel downregulated and upregulated microRNAs in idiopathic PAH patients, developed a 3-microRNA signature for diagnosis, and validated in vitro that miR-3168 targets BMPR2, thereby impairing angiogenesis.