To identify and characterize the etiological agent causing tilapia (Oreochromis niloticus) mortality in a lagoon located in Haikou, China, four isolates, designated ASL-1, ASB-2, ASB-3 and ASS-4, were recovered from moribund fish. They were gram-negative, motile, short and rod-shaped. Sequencing of the 16S rRNA gene, as well as of the housekeeping genes-dnaJ, elastase (ela) and gyrase subunit beta (gyrB), strongly indicated that the four isolates were identical to Aeronomas schubertii. A virulence test showed that ASS-4 was the most virulent, and the lethal dose (LD50) of 7 days was 4.91 × 104 CFU/g fish by intraperitoneal (i.p.) injection. Different infection routes with ASS-4 induced different mortality rates. Acute mortalities were present after both i.p. and intramuscular (i.s.) injections. Very low mortalities were observed after oral exposure, and no mortality was observed after immersion. This suggested that the natural infection routes of A. schubertii in tilapia might be through damaged body surface and/or digestive tract. The histopathology of challenged fish included livers showing vacuolation, spleens with hemorrhaging and brains with swelling capillaries. Antibiotic sensitivity testing indicated that ASS-4 was susceptible to norfloxacin and rifampicin but resistant to 10 different antibiotics. This is the first report that A. schubertii infected brackish water wild fish. This is also the first investigation of the possible entry routes of A. schubertii in fish. These results will shed light on the pathogenicity of A. schubertii and will help prevent and control A. schubertii infection in tilapia.