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We investigate upper crustal anisotropy of the Endeavour Segment of the Juan de Fuca Ridge using shear wave splitting measurements of ~3000 earthquakes recorded during three years using the Keck seafloor seismic network. We apply a new cluster analysis of shear-wave splitting measurements to our database. The methodology reduces the use of subjective criteria and improves the accuracy of measurements in the presence of noisy data. Fast polarization directions at a given seismic station are constant and stable during the deployment; however, fast-polarization directions between stations vary significantly. We presume that the lack of consistency of shear wave splitting among seismic stations reflects the spatial distribution of anisotropy in the vicinity of the ridge axis. We infer that the variation of fast polarization directions and delay times is caused by spatial variations in shallow hydrogeological structures and the stress field. Local faults and fissures are unlikely to be the primary cause of this anisotropy since most of the fast polarization directions are not consistent with the ridge parallel trend of faults. Stress perturbations induced by magmatic injection into the axial magma chamber or spatial variation in the rates of a hydrothermal heat transfer may contribute to the observed heterogeneity in seismic anisotropy.