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The aim of the present study was to evaluate the microbiological quality of rainbow trout meat treated with essential oils (EOs from <i>Citrus limon</i> and <i>Cinnamomum camphora</i>) at concentrations of 0.5% and 1.0% in combination with vacuum packaging during storage. The composition of the EOs were analyzed by gas chromatography coupled with mass spectrometry, and total viable counts (TVCs), coliform bacteria (CB), and lactic acid bacteria (LAB) were determined on the zeroth, first, third, fifth, and seventh days of storage at 4 °C. Individual species of isolated microorganisms were identified using a MALDI-TOF MS Biotyper. The results show that the major components of the EOs were linalool (98.1%) in <i>C. camphora</i> and α-limonene in <i>C. limon</i>. The highest number of TVCs and CB were 4.49 log CFU/g and 2.65 log CFU/g in aerobically packed samples at the seventh day. The lowest TVCs were those of samples treated with 1% <i>C. camphora</i> EO. For CB the most effective treatment was 1% lemon EO. LAB were only detected in a few samples, and were never present in aerobically packed samples; the highest number of LAB was 1.39 log CFU/g in samples treated with 1% lemon EO at day seven. The most commonly isolated coliform bacteria were <i>Hafnia alvei</i>, <i>Serratia fonticola</i>, <i>Serratia proteamaculans</i>, <i>Pantoea agglomerans</i>, and <i>Yersinia ruckeri. Lactobacillus sakei</i>, <i>Staphylococcus hominis</i>, and <i>Carnobacterium maltaromaticum</i> were the most frequently isolated bacteria from lactic acid bacteria. In conclusion, <i>C. camphora</i> EO at a concentration of 1% showed the highest antimicrobial activity.