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Gajami-sikhae is a traditional Korean fermented fish food made by naturally fermenting flatfish (<i>Glyptocephalus stelleri</i>) with other ingredients. This study was the first to investigate the diversity and dynamics of lactic acid bacteria in gajami-sikhae fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 4824 isolates were isolated from the fermented gajami-sikhae. These findings indicated that <i>Latilactobacillus</i>, <i>Lactiplantibacillus</i>, <i>Levilactobacillus</i>, <i>Weissella</i>, and <i>Leuconostoc</i> were the dominant genera during fermentation, while the dominant species were <i>Latilactobacillus</i> <i>sakei</i>, <i>Lactiplantibacillus</i> <i>plantarum</i>, <i>Levilactobacillus</i> <i>brevis</i>, <i>Weissella</i> <i>koreensis</i>, and <i>Leuconostoc</i> <i>mesenteroides</i>. At all temperatures, <i>L. sakei</i> was dominant at the early stage of gajami-sikhae fermentation, and it maintained dominance until the later stage of fermentation at low temperatures (5 °C and 10 °C). However, <i>L</i>. <i>plantarum</i> and <i>L</i>. <i>brevis</i> replaced it at higher temperatures (15 °C and 20 °C). The relative abundance of <i>L. plantarum</i> and <i>L. brevis</i> reached 100% at the later fermentation stage at 20 °C. These results suggest that the optimal fermentation temperatures for gajami-sikhae are low rather than high temperatures. This study could allow for the selection of an adjunct culture to control gajami-sikhae fermentation.