Endoribonuclease YbeY is essential for maturing ribosomal RNA in a wide range of bacteria. YbeY is specific to the single-stranded RNA of ribosomal RNAs and small RNAs. However, the structural relationship with the function and recognition of substrates remains elucidated. In this study, we overexpressed full-length YbeY from the gram-positive bacterium Staphylococcus aureus. The protein was purified and crystallized under conditions containing 0.1 M sodium citrate (pH 5.0) and 44% (w/v) polyethylene glycol 600. An X-ray diffraction dataset at a resolution of 1.9 Å was collected, and the dataset belonged to space group P6₃ with unit cell parameters a = 100.7 and c = 50.2 Å. The single-wavelength anomalous diffraction method was successful in determining the crystal structure. We are now refining the structure combined with structural analysis. The structure will provide molecular insights into the substrate recognition mechanism by showing the high-resolution features of the active sites.