In this study, the dark current-voltage characteristics of electron-only and hole-only poly(3-hexyl thiophene) (P3HT):[6,6]-phenyl C61-butyric acid methyl ester (PCBM) as a function of regioregularity (RR) and annealing time is investigated using the mobility edge (ME) model. This model is used to analyze the degradation of electron and hole mobilities as a function of annealing time for 93%-RR and 98%-RR P3HT:PCBM devices. The hole mobility is almost unchanged by the RR nature of P3HT and thermal annealing. The electron mobility, however, behaves differently after annealing. The electron mobility of 98%-RR devices, which is initially higher than that of the 93%-RR devices, experiences a steep decline with annealing. Based on ME analysis, this is due to an increase in trap states in the exponential tail caused by phase segregation of solid state blends of 98%-RR polymer and PCBM. The electron mobility of 93%-RR devices increases with annealing due to an optimization of nano-phase separated morphology.