Streptococcus agalactiae (also known as GBS) is an emerging pathogen of fish and is fatal to tilapia worldwide. However, the differences in pathogens-host interactions among different pathogenic GBS strains remain unclear. In this study, we investigated the dynamic bacterial colonization as well as microscopic lesions in multiple organs of tilapia infected with the low pathogenic TFJ0901 and high pathogenic THN0901 strains. Using the qPCR assay, we revealed that THN0901 can easily invade the spleen at the early stage of infection, and then effectively replicate in the brain and eyes, while bacterial loads are maintained at constant lower levels in all tissues of TFJ0901-infected fish at any time points. Both immunohistochemistry and histopathology showed that the differences in the microscopic lesions caused by the two strains were mainly focused on the blood vessels/sinusoids, and that THN0901 infection was more likely to lead to degenerative lesions within the endothelial cells, with subsequent vascular lesions and local tissue infarction, particularly in the brain, spleen, kidney and gills. THN0901 can also result in typical histopathological changes, including meningitis, epicarditis, and renal granuloma. In contrast, TFJ0901 caused slight or no microscopic lesions in those tissues over time. Interestingly, this study provides direct evidence that THN0901 can adhere to and invade the intestinal epithelial cells through intraperitoneal injection. Furthermore, touch impression smears of the spleen also confirmed that THN0901 can proliferate in macrophages and cause immune cells to collapse, whereas TFJ0901 did not appear to have the ability to do so. In summary, we closed a gap in understanding the differences in pathogen-host interactions between high and low pathogenic GBS strains, which will enhance our ability to develop an attenuated vaccine based on TFJ0901 in the future.