We investigated the primary mechanisms triggering the S-wave splitting (SWS) of seven unusually deep local earthquakes (between 50 and 60 km) which originated in the lithosphere beneath the Rwenzori region. We attempted to develop an understanding of the relationship between anisotropic structures in the lithosphere and tectonic deformation processes. A total of 12 out of 44 waveforms showed evidence of SWS on their polarization diagrams. The fast-wave direction (φ) and delay-time (δt) were estimated using the covariance matrix and the cross-correlation coefficient methods, respectively. We observed a clockwise rotation of φ-directions (NW - SE and ~ENE - WSW) at stations located in the rift valley. We related this pattern of φ-directions to anisotropic fabric, probably lattice-preferred orientation of preexisting olivine, whose a-axes are aligned with ESE absolute plate motion (APM) vector. At stations located outside the rift valley, however, we observed WNW - ESE and NNW - SSE patterns of φ-directions. We associated these patterns to the shape-preferred orientation of structures frozen in the lithosphere that are aligned with the present-day APM direction. We observed δt values ranging between 0.04 ± 0.01s and 0.43 ± 0.02 s, which decrease with distance away from the rift axis. This further supported our concept that the anisotropy observed at stations located on the moving plate is related to aligned melt inclusions frozen in the surrounding lithosphere. We further observed that the δt values increase linearly with ray-path length, which could indicate a fairly uniform anisotropy between 50-km and 60-km depth. Our study reported no evidence of multi-layer anisotropy beneath the Rwenzori region.