Early gender identification is essential in order to preferentially raise greater numbers of female sturgeon (Acipenseridae) for caviar production in aquaculture facilities. As many freeranging species of sturgeon are threatened or endangered, the ability to confirm gender antemortem can be critically important for conservation and recovery projects. The goal of this study was to compare the accuracy of non-invasive ultrasonography and minimally-invasive endoscopy for the identification in 140, three and four-year-old Siberian sturgeon (Acipenserbaerii), against the gold standard of gonadal biopsy and histology. Histology confirmed the gender for 128/140 (91.4%) fish. Histology and endoscopy agreed on the gender of 124/128 (96.9%) fish. Histology and ultrasonography agreed on 113/128 (88.3%) fish. Ultrasonography was significantly faster than endoscopy (11.8s versus 21.9s respectively). Endoscopy was more invasive but more accurate. The minor reduction in accuracy associated with non-invasiveultrasonography may be an acceptable trade-off in aquaculture and free-ranging applications.