Germline mutations in the bone morphogenetic protein type II receptor (BMPRII) gene play an essential role in the pathogenesis of familial pulmonary arterial hypertension (FPAH). In view of the histological similarities between scleroderma (SSc) and FPAH arterial lesion, we examined the expression levels of BMPRII in SSc microvascular endothelial cells (MVEC). Oxidative stress and serum starvation were used to examine apoptotic responses of MVECs. BMPRII expression levels were determined by RT‐PCR and by Western blot. Epigenetic regulation of BMPRII expression was examined by the addition of epigenetic inhibitors to MVECs cultures, by methylation‐specific PCR, and by sequence analysis of DNA methylation pattern of the BMPRII promotor region. SSc‐MVECs were more sensitive to apoptotic signals than were normal‐MVECs. A significant decrease in BMPRII expression levels in SSc‐MVECs was noted, whereas no significant differences in the expression levels of BMPRIA and BMPRIB were observed. Similar reduction in expression levels was noted in SSc skin biopsies. The expression level of BMPRII in SSc‐MVECs was normalized by the addition of 2‐deoxy‐5‐azacytidine and trichostatin A to cell cultures. Extensive CpG sites methylation in the BMPRII promoter region was noted in SSc‐MVECs with no detectable site methylation in control‐MVECs. SSc‐MVECs are more sensitive to apoptotic triggers than are control‐MVECs. The enhanced apoptosis may be related to epigenetic repression of BMPRII expression as apoptosis of control‐MVECs can be augmented by knocking down BMPRII expression. The role of BMPRII underexpression in the pathogenesis of SSc vasculopathy is suggested and should be investigated further.