Sea urchins mineralize Mg-calcite skeletons, both, within their exoskeletons as well as in their spines. In this study we have investigated sea urchin spines of the species Amblypneustes pachistus. The spines are round and consist of several wedges that extend from the base to the tip of the spine. The wedges are connected to each other by porous calcite. Rocking curves of the spines show a distribution of 0.5° of the 110 reflection, with the domains being misoriented by 0.1° to each other. In our EBSD system the average mean angular (MAD) deviation is 0.3°. This is higher than the signal that is needed for the detection of small misorientations of domains within a sea urcin spine. In order to increase the precision (not the accuracy) of the EBSD measurements several factors, such as geometric artifacts and charging of calcite were minimized. Handling of these factors and utilizing the subsequently described statistical approach allowed for the identification of different domains within the spines. It further allowed calculating the degree of misorientation between these domains. Our EBSD analyses and the subsequent evaluation of the data show that the wedges forming the spines of Amblypneustes pachistus are mosaic crystals. The misorientation of the wedges to each other increases from the base of the spine towards its tip. The here proposed method for increasing the precision of the angular resolution showed reproducibility on silicon of 0.05°.