Abstract Dislocations and planar faults are found to develop in the Mo 5SiB 2 phase during elevated temperature annealing. The dislocations formed in Mo 5SiB 2 of annealed alloys are mostly edge dislocations with the Burgers vectors of 〈100], 1/2〈111], and 〈110]. For the Mo-rich Mo 5SiB 2 phase that formed in a Mo–10Si–20B alloy, a significant amount of constitutional vacancies is introduced during solidification, and the excess vacancies aggregate and collapse into dislocations. At the same time, these dislocations can act as the heterogeneous nucleation sites for the subsequent Mo precipitation. For the Mo-lean Mo 5SiB 2 phase that formed in a Mo–13Si–28B alloy, the constitutional defects are not significant for the development of dislocations.