Fish mucosa and their commensal microbiota serve as the first biological bulwark against invading pathogens. The purpose of this study is to study the implications on tilapia health status of the associated commensal microorganisms. Illumina sequencing was used to study the difference between the microbiota of mucosal surfaces from healthy tilapia, live and dying tilapia after Streptococcus agalactiae infection. The results showed that there were several genera dominated on tilapia skin and gill surfaces, i.e., Truepera, Thiobacillus, Arcobacter, Marinomonas, and Vibrio. There was no significant difference between the skin and gill microbiota of the live tilapia after Streptococcus agalactiae infection and those of the initial tilapia sample. A decreased bacterial diversity was shown in the skin and gill microbiota of the dying tilapia after the pathogen infection, and the genera of Arcobacter, Pseudoalteromonas, Marinomonas, Pseudomonas and Vibrio were decreased, while the genus of Streptococcus dominated in the skin and gill microbiota of the dying tilapia after the pathogen infection, with the relative abundance of 55.30%±1.24%. The results suggested that commensal microbiota of tilapia skin and gill surface could be related to fish health.