Ruegeria atlantica and Pseudoalteromonas neustonica are fish gut bacteria which have been isolated from the gut of Pagrus major and Acanthopagrus schlegelii, respectively. Total 24 compounds (1–24) were isolated from these two bacteria; 18 compounds (1–18) from R. atalantica and six compounds (19–24) from P. neustonica. Their chemical structures were elucidated by spectroscopic and spectrometric data analysis and chemical synthesis. Compounds 11 and 13 showed strong collagenase inhibitory activity with 31.91 and 36.43% at 20 µM, respectively, comparable to or surpassing that of the positive control, epigallocatechin gallate (EGCG, 34.66%). Also, compounds 11, and 14 exhibited mild tyrosinase inhibitory effect with 6.73 and 13.68%, respectively. All the tested compounds displayed no significant antibacterial activity against Escherichia coli and Bacillus subtilis up to 100 µM. The collagenase- and tyrosinase-inhibitory compound 11, cyclo(l-Pro-d-Leu), were found to be stable under heat (50°C) and UV light (254 and 365 nm) for up to 7 days. These results indicate that compound 11 could be developed to a cosmeceutical with anti-aging effect.