Five possible probiotic strains (Bacillus siamensis LF4, Micrococcus yunnanensis LD5, Micrococcus aloeverae LC3, Mitsuaria chitosanitabida LD3 and Lactococcus petaurid LF3) were previously isolated from the intestine of Japanese seabass (Lateolabrax japonicus). A feeding trial was performed to evaluate the effects of dietary administration of the five potential probiotic bacteria on growth performance, digestive enzyme activities, immune response, antioxidant capability and ammonia tolerance in juvenile Japanese seabass (L. japonicus). The fish were fed for six weeks with control diet (C, without probiotics) or diets supplemented with 1 × 108 CFU/g of B. siamensis LF4 (T1), Lc. petaurid LF3 (T2), M. chitosanitabida LD3 (T3), M. aloeverae LC3 (T4) and M. yunnanensis LD5 (T5), respectively. Above 93.33% survival rate was in the control and treatments, indicating that the five potential probiotics are safe for Japanese seabass. Supplementation of probiotics (except M. aloeverae LC3) also significantly improved weight gain rate and specific growth rate of Japanese seabass, and B. siamensis LF4 significant enhanced the feed intake of fish (p < .05). Significantly increased trypsin activity was detected in fish fed B. siamensis LF4 (T1) and Lc. petaurid LF3 (T2)-containing diets, while B. siamensis LF4 significantly boosted amylase activity (p < .05). Overall, B. siamensis LF4 and Lc. petaurid LF3-supplemented groups (T1 and T2) were noticed with improved antioxidant and innate immunity by evaluating relative indictors, that is total antioxidant capacity (T-AOC), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), lysozyme, complement 3 (C3), glutamic–oxalacetic transaminase (GOT) and glutamic–pyruvic transaminase (GPT) levels. The cumulative mortality of Japanese seabass, experimentally exposed to ammonia (80 mg/L) for 96 h, was significantly lower in fish fed diets T1 and T2 as compared to control and other experimental diets. In summary, host-associated B. siamensis LF4 and Lc. petauri LF3 could be applied as probiotics for improving growth performance, innate immunity, antioxidant activity and ammonia tolerance in juvenile Japanese seabass (L. japonicus).