Abstract:[Objective] To investigate the effect of the bio-organic fertilizer on heart rot and rhizosphere bacteria of pineapple. [Methods] Through high-throughput sequencing, we explored the bacterial diversity and community in rhizosphere of pineapple applied with different fertilizers. [Results] Compared with conventional fertilizer treatment (CK) and common organic fertilizer treatment (YJ), bio-organic fertilizer treatments of KN (sheep manure+peat soil+Bacillus subtilis) and KY (sheep manure+coconut chaff+B. subtilis) significantly reduced the incidence of heart rot in pineapple, especially KN. The α diversity of soil in KN and KY was higher than that of CK and YJ and a significantly different bacterial community structure emerged in the two bio-organic fertilizer treatments. Compared with CK, KN significantly increased the abundance of Bacteroidetes and Firmicutes, while the abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Nitrospirae in KY was significantly raised. At the genus level, the abundance of both Paraburkholderia and Flavobacterium in the bio-organic fertilizer treatments was significantly elevated. Variance partitioning analysis suggested that soil chemical properties (36.29%) had the greatest influence on the bacterial community, particularly soil available potassium and organic matter. In addition, the incidence (22.53%) and partial productivity of fertilizer (16.42%) were also the key influencing factors.[Conclusion] The application of bio-organic fertilizers (KN, KY) can change bacterial community structure in rhizosphere of pineapple and decrease the incidence of heart rot, which are important for the rhizosphere ecosystem stability and health of pineapple.