The widespread use of smartphones has led to the emergence of new mobile learning tools. The aim of this study was to compare traditional methods to mobile learning applications, and their effect on the academic achievement and anxiety levels of students learning genital system anatomy. This research study was a randomized controlled study conducted with students who took anatomy between November and December 2018. The cohort consisted of 63 students who met the sampling criteria. Groups (control = 31, experimental = 32) were randomly selected using a simple number table. The mobile application developed for the experimental group was installed on the students' mobile devices with the extension "genitalsystem.apk." The anatomy of the genital system was taught to the control group using the standard curriculum and to the experimental group using the mobile application. After teaching the anatomy of the genital system, the state anxiety levels of the students in the control group were determined to be higher at 45.6 (±8.7) than the experimental group at 40.4 (±8.3) as measured by the 20-80 point STAI scale. The posttest examination average of the control group was 8.9 (±6.9) out of 22 or 40.4 (±6.9)% and the posttest average of the experimental group using mobile application was 14.9 (±5.5) or 67.7 (±5.5)%. State anxiety levels and examination grades showed a highly significant difference in favor of the experimental group. These results indicate that using mobile applications when teaching anatomy may be an effective method to enhance learning and reduce anxiety levels when compared to the traditional teaching methods.