Tilapia is one of the most important aquaculture resources globally, playing a vital role in food security and economic development. In many developing countries, such as Mexico, tilapia is the most widely farmed and consumed fish. One of the primary challenges that the tilapia culture faces is the occurrence of infectious diseases, particularly those caused by bacterial pathogens. Motile Aeromonas Septicaemia (MAS) is a disease of tilapia caused by different species of the genus Aeromonas , which causes mass mortalities and economic losses. Identifying the molecular mechanisms behind natural susceptibility or resistance in different tilapia populations of commercial interest is key for the development of resistant lines. In the present study, Aeromonas veronii was isolated and confirmed as the cause of natural infections in a hybrid red tilapia i.e., “Pargo -UNAM” in Mexico by molecular identification using gyrB gene. Assessment of the differential survival rate between Pargo-UNAM and wild-type Nile tilapia ( O. niloticus L .) under controlled experimental conditions confirmed a higher susceptibility of the hybrid red tilapia compared to wild-type Nile tilapia. Histopathology revealed lesions consisting with MAS. Finally, the transcriptional changes induced in the spleen of the challenged organisms were studied. The transcriptomic profiling revealed that wild-type Nile tilapia displays a higher number of genes related to external stimuli and bacterial response than hybrid red tilapia Pargo -UNAM during infection with virulent Aeromonas veronii. These results represent a step forward toward the development of MAS-resistant tilapia lines as a strategy to control and prevent this disease.