By comparing the changes of the microflora during salted-dried processing of the red-fleshed fish (Decapterus maruadsi) and the white-fleshed fish (Trichiurus lepturus), the dominant bacterium with antioxidant activity was also studied. In this paper, MiSeq sequencing technology was utilized in two kinds of fish in different processing phases. The results showed that the microflora of the two fishes was mainly distributed in Bacteroidetes and Proteobacteria. At the family level of the initial material, there were 7 and 15 colonies in D. maruadsi and T. lepturus, respectively. All the species in round scad were totally in T. lepturus and Enterbacteriaceae was as common dominant bacteria, accounted for 47% and 26% in D. maruadsi and T. lepturus respectively. From the start of salting, the number of bacteria in both fishes was greatly reduced. Vibrionaceae and Bacillaceae were the common dominant bacteria, the former accounted for an average of 40.3% and 42.2% of D. maruadsi and T. lepturus, and the latter accounted for an average of 16.7% and 13.3%. Among the raw materials, four spoilage bacteria of Enterobacteriaceae, Pseudomonas, Vibrionaceae, and Shewanellaceae were showed in both fishes. The dominant spoilage bacteria in both fishes during salt-dried processing was Vibrionaceae. Lactic acid bacteria (LAB), including Streptococcaceae and Lactobacillaceae, only appeared in T. lepturus. Therefore, during salt-dried processing, the degree of reduction of bacteria in hairtail was greater than that of round scad, and they all showed a decrease. The two fishes contained common bacteria and dominant bacteria, but showed significant differences. The spoilage bacteria of both fishes have been greatly reduced, suggesting that salt-dried processing is beneficial to reducing the possibility of fish corruption. T. lepturus could be selected for LAB isolation for subsequent antioxidant studies.