RationaleIt is imperative to understand how chemical preservation alters tissue isotopic compositions before using historical samples in ecological studies. Specifically, although compound‐specific isotope analysis of amino acids (CSIA‐AA) is becoming a widely used tool, there is little information on how preservation techniques affect amino acid δ15N values.MethodsWe evaluated the effects of chemical preservatives on bulk tissue δ13C and δ15N and amino acid δ15N values, measured by gas chromatography/isotope ratio mass spectrometry (GC/IRMS), of (a) tuna (Thunnus albacares) and squid (Dosidicus gigas) muscle tissues that were fixed in formaldehyde and stored in ethanol for 2 years and (b) two copepod species, Calanus pacificus and Eucalanus californicus, which were preserved in formaldehyde for 24–25 years.ResultsTissues in formaldehyde‐ethanol had higher bulk δ15N values (+1.4, D. gigas; +1.6‰, T. albacares), higher δ13C values for D. gigas (+0.5‰), and lower δ13C values for T. albacares (−0.8‰) than frozen samples. The bulk δ15N values from copepods were not different those from frozen samples, although the δ13C values from both species were lower (−1.0‰ for E. californicus and −2.2‰ for C. pacificus) than those from frozen samples. The mean amino acid δ15N values from chemically preserved tissues were largely within 1‰ of those of frozen tissues, but the phenylalanine δ15N values were altered to a larger extent (range: 0.5–4.5‰).ConclusionsThe effects of preservation on bulk δ13C values were variable, where the direction and magnitude of change varied among taxa. The changes in bulk δ15N values associated with chemical preservation were mostly minimal, suggesting that storage in formaldehyde or ethanol will not affect the interpretation of δ15N values used in ecological studies. The preservation effects on amino acid δ15N values were also mostly minimal, mirroring bulk δ15N trends, which is promising for future CSIA‐AA studies of archived specimens. However, there were substantial differences in phenylalanine and valine δ15N values, which we speculate resulted from interference in the chromatographic resolution of unknown compounds rather than alteration of tissue isotopic composition due to chemical preservation.