Carbon quantum dots (CDs) were widely investigated because of their tunable fluorescence properties and low toxicity. However, so far there have been no reports on in vivo functional studies of hair and skin derived CDs. Here, hair derived CDs (HCDs) and skin derived CDs (SCDs) were produced by using human hair and pig skin as precursors. The quantum yields (QYs) of HCDs and SCDs were quite high, compared to citric acid derived CDs (CCDs). HCDs and SCDs possess optimal photostability, hypotoxicity and biocompatibility in zebrafish, indicating that HCDs and SCDs possess the capacity of being used as fluorescence probes for in vivo biological imaging. The long-time observation for fluorescence alternation of CDs in zebrafish and the quenching assay of CDs by ATP, NADH and Fe3+ ions demonstrated that the decaying process of CDs in vivo might be induced by the synergistic effect of the metabolism process. All results indicated that large batches and high QYs of CDs can be acquired by employing natural and nontoxic hair and skin as precursors. To our knowledge, this is the first time to report SCDs, in vivo comparative studies of HCDs, SCDs and CCDs as bioprobes, and explore their mechanism of photostability in zebrafish.