Evaluation of two quantitative PCR assays using Bacteroidales and mitochondrial DNA markers for tracking dog fecal contamination in waterbodies

► Two qPCR assays for tracking dog fecal contamination in waterbodies were compared. ► The Bacteroidales and the mtDNA markers had equally high (> 90%) sensitivity. ► The mtDNA marker was superior for specificity. ► The Bacteroidales marker exhibited a faster decay in freshwater microcosms. ► Rare detection of the markers in urban water samples suggests low contamination levels.