In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – array-based hybridization capture and in-solution capture using either RNA or DNA baits – have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits. , METHOD SUMMARY We compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity and reproducibility for ancient and modern Mycobacterium leprae and Treponema pallidum samples. The three methods – array-based capture and in-solution capture with RNA and DNA baits – were all tested in three independent replicates.