In this paper, we describe a new non-damaging internal tissue sampling method for preserved collection of teleostean specimens. It was tested on freshwater pipefish, as external tissue sampling is made difficult by the lack of scales, the lack of pelvic fins, the atrophy of pectoral and anal fins. The internal tissue is detached by scratching the inside of the urogenital papilla with a fine metallic probe. 95% ethanol is injected using a fine syringe, and then sucked back into the syringe with the detached tissue. This protocol has been tested on 6 specimens from 5 species of pipefish. For each specimen DNA was extracted from the internal tissue, a caudal fin clip, and when possible, eggs sampled from the male brooding pouch. Partial Cytochrome c oxydase I (COI) was amplified and sequenced. For each specimen, the 582 bp long sequences obtained from the internal tissue, the fin clip and the eggs were identical. These results validate this non-damaging internal tissue sampling method, which leaves absolutely no trace on the specimen. Although this method was developed on pipefish, it could be applied to other teleostean, even precious museum collection specimens such as type specimens. The aim of this paper, using the example of freshwater pipefish, is to present this method, which aims at preserving precious collection specimens while still valorising them.