Huge feed volume and shrimp density loading in the intensive shrimp culture decreased water quality. Ammonia and nitrite, which are toxic substances, are occurred from feed and shrimp excretion. Bacillus and related genera (class Bacilli) are bacteria capable of transforming ammonia to nitrite and then nitrite to nitrate by nitrification. In this study, wild marine Bacilli were isolated from samples collected from seagrass beds Andaman Sea, Thailand. Bacilli strains were obtained by using the heat-shock method. Three bacilli bacteria were consisting of Bacillus sp. BC02 (DNA-based), Bacillus sp. BC05 (morphology-based) and Virgibacillus sp. BC06 (DNA-based) was obtained. This study aims to investigate these isolates in shrimp wastewater improvement compared with the commercial seed of Bacillus spp. product (PM-1). Seven wastewater treatments were separately tested by adding different formulas of bacteria. Each treatment was added for 1% (w/v) of 107 CFU/mL density and incubated for 7 days. Treatment of BC02+BC05 showed a significant TSS decrease (66.56%) and produced the highest nitrate concentration. The highest increase of OTP (84.97%) was found in the treatment of BC02+BC05+BC06. PM-1 product has presented the best BOD lessening (54.35%) and showed a non-significant reduction of ammonia (98.60%) with the highest nitrite (0.685 ± 0.009 mg/L) at the end of the experiment. Virgibacillus (BC06) has resulted in the highest significant reduction of COD (60.39%). Thus, it might be summarized that three marine isolates of Bacillus, Virgibacillus, and commercial PM-1 product have excellent potential to improve wastewater quality with no significant diferent. Marine Bacilli can be substitution used for commercial PM-1 products.