Basaloid squamous cell carcinoma of the oesophagus (BSCCE) has poorer prognosis than conventional oesophageal squamous cell carcinoma (ESCC). This study is the first report on highly expressed miRNAs in BSCCE and their target genes. BSCCE and ESCC patients who underwent esophagectomy were selected for this study. Total RNA was extracted from formalin-fixed paraffin-embedded blocks to examine expression of miRNAs and target genes. miRNA mimic or inhibitor transfected cells were used in validation experiments. miRNA and mRNA quantification were performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). miRNA microarray analysis revealed four candidate miRNAs. Further investigations including cell line experiments demonstrated that miR-3687 was a candidate miRNA and progesterone receptor membrane component2 (PGRMC2) was its target gene. PGRMC2 was found to be related to cell proliferation and local progression. miR-3687 may be a candidate miRNA conferring BSCCE aggressiveness, and PGRMC2 is one of its target genes. Copyright© 2019, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.