Deep learning has gained considerable interest in agricultural breeding research. While advances in sequencing technologies have made genotypic data collection easier in genomic breeding, phenotypic data collection remains labor intensive and time consuming. Furthermore, as traditional phenotypic data collection relies heavily on manual processes, the results may vary based on the researcher’s skill and criteria. Thus, automated phenotypic data collection is essential for addressing these challenges. In this study, we aimed to develop a deep learning model using the YOLOv8 framework to measure the lengths of hypocotyls and roots in sprout vegetables such as mung bean, cowpea, and soybean. Our model automates the measurement process, accurately identifies the hypocotyl and root using Roboflow, and subsequently measures their lengths with high precision in various legume species. This approach addresses the challenges of extensive phenotypic data collection, which is essential for genetic breeding and agricultural improvement. Our deep learning model facilitates consistent and accurate data collection in large-scale studies by controlling variables influenced by the researcher’s skills and criteria. This reduces errors and enhances data reliability and accuracy, which are crucial for successful breeding practices and agricultural research.