Different modalities such as lectures, dissections, 3D models, and online learning are used for teaching anatomy. To date, online learning has been considered a useful additional didactic tool. This study aimed to compare veterinary students’ performance in radiographic anatomy (radio-anatomy) after online or classroom-based teaching to assess the extent to which the two methods were interchangeable. Three strategies were compared in a cohort of 83 learners. Students were committed to online learning only, online learning with the use of specimen equine bones, or learning on conventional radiographs with specimen equine bones. At baseline (pre-test), scores from a mental rotation test and radio-anatomy knowledge test were similar between groups. After training (post-test), scores in mental rotation and radio-anatomy significantly increased by 6.7/40 units (95% CI: 5.2–8.2; p < .001) and 5.1/20 units (95% CI: 4.3–5.9; p < .001), respectively. There was no difference in scores for mental rotation and radio-anatomy knowledge between groups at post-test. Gender influenced the mental rotation, with men scoring significantly higher than women at pre-test (M = 23.0, SD = 8.8 vs. M = 16.5, SD = 6.9; p = .001) and post-test (M = 32.1, SD = 5.5 vs. M = 22.7, SD = 8.6; p < .001). However, radio-anatomy knowledge was not influenced by gender. These results suggest radio-anatomy teaching can be safely achieved with either conventional radiographs or online resources. This is of interest since, due to the COVID-19 outbreak, rapidly changing from on-site to online methods for teaching veterinary medical education proved necessary.