AbstractEarly detection of invasive species is crucial for effectively controlling the potential damage they can inflict on the ecosystems. In contrast to the many limitations that conventional detection methods like visual surveys and netting hold, environmental DNA assay provides a powerful alternative. This non‐invasive, highly sensitive, and user‐friendly technique offers the advantage of detecting invasive species even in areas where direct observation is challenging, thus addressing the shortcomings of traditional techniques and enhancing overall accuracy in estimating distribution. The spread of invasive Pterygoplichthys sp. has become a cause for concern in biodiversity‐rich countries like India. Despite this, comprehensive studies on the prevalence of this invasive species are limited. The Eastern Ghats of India remain under‐explored with a high potential for supporting diverse lifeforms. Studying the extent of biological invasions in the Eastern Ghats is essential for effective management and to mitigate the ecological and socioeconomic impacts of invasive species. In this study, we have designed and optimized an eDNA‐based quantitative PCR assay to map the presence and spread of invasive Pterygoplichthys sp. in selected freshwater ecosystems of the Eastern Ghats. This assay detected invasive Pterygoplichthys sp. in almost 65% of the total locations sampled. This study can be further extended to larger geographical areas, which can contribute to formulating necessary measures by the authorities to manage invasion and conserve the diversity of the freshwater ecosystem.