We apply for the first time transmission electron microscopy to the direct observation of the deep-UV nonlinear optical crystal KBe
2BO
3F
2 (KBBF) grown using different methods. Two kinds of electron diffraction patterns were observed in the hydrothermally synthesized KBBF along the [120] direction, which resulted from the coexistence of two structures with space groups R32 and R
c. As a comparison, the flux grown KBBF crystals show uniform R32 structures. Furthermore we observed a twin boundary in flux KBBF which corresponds to the (2
3)
R32 crystallographic plane. Two structure models are proposed here for the twin boundary. These observations on the microstructure and defects were not disclosed in previous powder XRD and optical microscopy experiments and shed new light on the understanding of the structure and defects of KBBF crystals.