The crystal structure of a pale blue transparent Mn-rich fluorapatite (MnO: 9.79 wt%) with the optimized formula ~(Ca8.56Mn2+1.41Fe2+0.01)P6O24F2.00 and space group P63/m, a = 9.3429(3), c = 6.8110(2) Å, Z = 2 has been refined to R = 2.05% for 609 unique reflections (MoKα). The Mn in the Eibenstein an der Thaya, Austria apatite is strongly ordered at the Ca1 site: Ca1: Ca0.72(1)Mn0.28, Ca2: Ca0.96(1)Mn0.04. There is a linear variation in <Ca1-O> as a function of Mn content (r2 = 1.00). The dominant band in the optical absorption spectrum of fluorapatite from Eibenstein is in the 640 nm region with E || c > E ⊥ c. The 640 nm band is attributed to Mn5+ at the P site by analogy with previous studies. This interpretation is consistent with studies of well-characterized synthetic materials of the apatite structure that contain Mn5+. Because Mn5+ has intense absorption in the visible region of the spectrum, if a small proportion of the total Mn is Mn5+ at the P site, that substituent dominates the spectrum and the color of the mineral. To determine if the pale blue color is due to radiation effects, a fragment of the fluorapatite crystal was heated at 400° C for 1 hour, and the change in color was slight. All of these observations are consistent with the origin of color from Mn5+. Assuming that all the intensity of the 640 nm (E || c) absorption is from Mn5+, the concentration of Mn5+ in this fluorapatite sample was calculated as 2.6% of the total manganese content (~P5.96Mn5+0.04). The calibration was estimated from the spectrum of the related compound Sr5(P0.99Mn5+0.01)3Cl. The weak band at about 404 nm in the E || c spectrum may be the corresponding band for Mn2+ in octahedral coordination.