This paper examines the evolution of FAAs in hake stored in ice and kept in controlled atmospheres for 33 days with four different gas mixes (CO2/O2/N2): M1 (60/15/25), M3 (40/40/20), M4 (60/40/0), and M5 (40/60/0). The most abundant FAAs in hake muscle are threonine, glutamic acid, glycine, alanine, β-alanine, tryptophan, 1-methylhistidine, and anserine. Anserine was the compound initially present in the highest concentration (61.65 mg/100 g of fish wet weight). As storage progressed, anserine concentrations fell, the smallest decrease being found in the lot kept in M1. At the end of storage the lot with the lowest level of anserine was M5C, which contained the highest O2 levels. The levels in the other lots were very similar. This fall in anserine coincided with an increase in 1-methylhistidine and β-alanine, the two amino acids to which it becomes hydrolyzed. As well as the fall in anserine, there was a progressive increase in muscle tryptophan during storage of the hake. This increase became more pronounced from day 12 of storage and was greatest in the control and lots M1C and M3C, which relates to the results of the other biochemical indexes. Both anserine and tryptophan could be used as quality control indexes for chilled hake. In general, no clear relationship was found between the effect of the atmosphere and the behavior of the FAAs.