Photodarkening-induced output power degradations and long-term stability in high power pulsed and CW fiber laser MOPA systems are discussed. The studied laser systems are based on aluminosilicate single-mode Yb-doped fibers and use the GTWave fiber technology for cladding pumping. The active fiber lengths are between 10-30m. We have tested Yb-doped fiber amplifiers operated under both pulsed and CW mode. Using OTDR background-loss measurements we show, for the first time, that the photodarkening-induced loss is non-uniformly distributed along the length of the active fiber. By calculating the average inversion along the fiber length, we show that the induced loss follows closely an Yb-inversion dependence to the power of 2. In addition we have studied the temperature dependence of the output power variation. It is shown that increasing (decreasing) operating temperature results in decrease (increase) of the laser output power, reaching the new equilibria over time scales of ~200hours. We also present data on the non-photodarkening SPI fiber which is used in all SPI products.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.