Nitrogen (N) is an essential nutrient for plant growth and tuber yield in potato. Its excess application is harmful for environment, and therefore dissecting traits involved in improving nitrogen use efficiency (NUE) and yield is essential to address them. This study was conducted to analyze variation in 56 Indian potato varieties at optimal N concentration (2 milli molar) under aeroponics for two years based on 17 different traits for root system architecture (length, surface area, diameter and volume), plant height, leaf area, root and shoot dry weight, tuber traits (number, yield and dry matter), and NUE parameters viz., NUE, agronomic NUE (AgNUE), nitrogen uptake efficiency (NUpE), nitrogen utilization efficiency (NUtE), harvest index (HI) and N harvest index (NHI). Significant differences (p < 0.05) were observed in the varieties for most traits under the investigation. The Agglomerative hierarchical clustering (AHC) analysis clearly distinguished the varieties into two main groups, and principal component analysis (PCA) analysis showed total 64.78% variability in the first two components. Significant and positive correlations were found for tuber yield with AgNUE, NUE and NUpE. On the other hand, top 10 promising varieties under aeroponics for above traits were Kufri Badshah, Kufri Frysona, Kufri Chipsona-3, Kufri Pushkar, Kufri Lalit, Kufri Ashoka, Kufri Sutlej, Kufri Jyoti, Kufri Mohan and Kufri Khyati. This study implies that a great variation exists in the Indian potato varieties including old and new categories and they can be exploited in breeding for increasing resource capture to improve NUE in potato.