Background <p>The Asian elephant, a keystone species of immense ecological and evolutionary significance, is under intensifying threat from habitat fragmentation and human-elephant conflict. Reliable population estimates are critical for effective conservation planning and understanding demographic processes, yet traditional methods like dung counts can be skewed by detectability issues and environmental variability. Here, we compared conventional line-transect dung counts with a non-invasive genetic spatially explicit capture-recapture (genetic SECR) approach in Kodagu, Karnataka, using high-throughput microsatellite sequencing (SSR-Seq). Our study area harbours a known population of 34 elephants (0.21 elephants/km²), providing a rare opportunity to evaluate the accuracy and bias of estimation methods against a field-validated reference point.</p> Results <p>Dung counts yielded an elephant density of 1.27(±0.32) elephants/km², overestimating the true population by 6 times. In contrast, genetic SECR based on genotypes from 131 fecal samples estimated a density of 0.23 elephants (±0.03)/km² individuals), closely aligning with the known density. Genetic analysis also revealed substantial allelic richness and potential population substructure.</p> Conclusions <p>These results demonstrate that genetic SECR not only reduces estimation bias but also reveals evolutionary relevant insights into genetic diversity and population structure. While genetic methods require greater per-unit investment compared to dung counts, a hybrid strategy may be most practical: periodic genetic SECR surveys to calibrate and validate easier methods (like dung counts or camera traps) used more frequently. As technology advances, costs of fecal DNA analysis are likely to decrease further. This hybrid framework optimizes resource allocation while maintaining scientific rigor, particularly important for large-scale monitoring programs across diverse landscapes</p>