[Objective] To compare the biotite weathering activities and mechanisms betweenPseudomonas azotoformans F77 andPseudomonas paracarnis P1. [Methods] During the mineral weathering process, the dissolved Fe and Al concentrations, cell number, pH, gluconic acid concentration, and residual glucose concentration in the culture medium were determined to reveal the biotite weathering effects and mechanisms of strains F77 and P1. Furthermore, RNA-seq was employed to explore the molecular mechanism for the difference in the biotite weathering effect between the two strains. [Results] During the 5 days of mineral weathering, strain F77 increased Fe and Al concentrations by 3.3−23.3 folds and gluconic acid concentration by 27.3−53.9 folds the compared with strain P1. Meanwhile, strain F77 showed decreased cell number and medium pH compared with strain P1. The data of comparative transcriptomics showed that strain F77 had more specific genes (2 872) and differentially expressed genes (1 832) than strain P1 (1 903 and 1 258 genes, respectively). Additionally, strain F77 carried more genes involved in the membrane transport, carbohydrate metabolism, cell motility, chemotaxis, and signal transduction than strain P1. Furthermore, strain F77 had higher fold changes in the expression levels of superoxide dismutase and catalase genes as well as higher number and fold changes of the genes involved in gluconic acid synthesis than strain P1. [Conclusion] Strain F77 surpassed strain P1 in weathering the biotite and producing gluconic acid. Strain F77 promoted the biotite weathering by producing gluconic acid. The addition of biotite significantly up-regulated the expression of genes involved in the transmembrane transport, cell movement and chemotaxis, signal induction, and carbon and energy metabolisms in mineral weathering. Furthermore, the genes involved in gluconic acid synthesis and encoding superoxide dismutase and catalase may play a role in the mineral weathering by strain F77.