Abstract
<jats:p> Chinese Bahaba ( <jats:italic>Bahaba taipingensis</jats:italic> , Sciaenidae) is a Critically Endangered, Grade I state protected marine fish in China. Reliable, non invasive monitoring tools are urgently needed to inform conservation and restocking efforts. We developed and validated three TaqMan probe–based qPCR assays targeting mitochondrial 12S rRNA, ND5, and control region (D–loop) loci for species specific detection of B. taipingensis. Primer–probe sets were designed from complete mitochondrial genomes and evaluated in silico against GenBank and in vitro against tissue DNA from <jats:italic>B. taipingensis</jats:italic> and closely related sciaenids, plus positive eDNA samples; sensitivity was quantified using serial dilutions of synthetic target DNA. All three assays showed high specificity and consistent amplification; 12S rRNA assay (Bhb–12S) was selected for field screening based on superior low copy sensitivity and minimal by products. We applied the Bhb–12S assay to 414 seawater samples collected from 23 sites in western Hong Kong during 2025 surveys, detecting <jats:italic>B. taipingensis</jats:italic> eDNA in the September samples (0.71–2.85 copies per μL; mean 2.05), with positive detections confirmed by Sanger sequencing. Overall, these validated qPCR assays provide a robust molecular toolkit for non invasive monitoring of <jats:italic>B. taipingensis</jats:italic> and will aid conservation planning, restocking evaluation, and long term biodiversity assessments in the Pearl River Estuary and adjacent coastal waters. </jats:p>