In aquaculture, antibiotics are commonly used to provide protection against pathogens; however, this practice has become controversial due to increased occurrences of microbial resistance, and alternatives are needed. This study aimed to investigate the antimicrobial activity of yeast glycoprotein (YG) against
Aeromonas caviae
. Pathogens were isolated from liver of diseased
Carassius auratus gibelio
. Based on morphological and biochemical analysis, together with 16S rRNA gene sequencing, the isolated strains were identified as
A. caviae
and concluded as clones of a single strain and named L2. Further pathogenicity analysis revealed that
A. caviae
possessed β‐haemolysis, and its median lethal dose for
C. gibelio
was 1.33 × 10
6
CFU/ml. Hepatic adenylate kinase and pyruvate kinase activities of
C. gibelio
were inhibited post–
A. caviae
infection. Antimicrobial drug test suggested that
A. caviae
was a multidrug‐resistant organism but could be inhibited by YG in vitro. Minimum inhibitory and bactericidal concentration of YG was 83.3 mg/ml and 166.7 mg/ml, respectively. Microbiota sequencing results showed that YG supplement could obviously decrease the relative abundance of
Aeromonas
and increase the microbial diversity. Our study revealed that
A. caviae
from
C. gibelio
was a multidrug‐resistant bacteria strain, and could be significantly inhibited by YG in vivo and in vitro, thus providing important insights into ecological control and pathogenesis of
A. caviae
in aquaculture.