Background Diversity of the microbiota, which is essential for lower airway homeostasis, is greatly altered in acute respiratory distress syndrome (ARDS). Extracorporeal membrane oxygenation (ECMO) is the ultimate protective treatment for the lungs of patients with severe ARDS, but little is known about its effect on the lung microbiota of these patients. The aim of this study was to evaluate the effect of ECMO on the lung microbiota of ARDS patients. Methods This was a prospective, observational clinical study of ARDS patients with COVID-19. We performed 16S rRNA and fungal ITS1 profiling and shotgun sequencing on bronchoalveolar lavage fluid (BALF) samples collected from patients with ARDS due to COVID-19. Results BALF was collected from 13 patients, five of whom underwent ECMO. The median age of the patients with ECMO was significantly younger than that of those without ECMO (44 [IQR: 36-48] years vs. 64 [IQR: 53-74] years, p