The literature shows that aerosol optical depth (AOD) derived from the MODIS Collection 5 (C5) dark target algorithm has been extensively validated by spatiotemporal collocation with AERONET sites on both global and regional scales. Although generally comparing well over the eastern US region, poor performance over mountains in other regions indicate the need to evaluate the MODIS product over a mountain site. This study compares MODIS C5 AOD at 550nm to AOD measured at the Appalachian State University AERONET site in Boone, NC over 30 months between August 2010 and September 2013. For the combined Aqua and Terra datasets, although more than 70% of the 500 MODIS AOD measurements agree with collocated AERONET AOD to within error envelope of ± (0.05 + 15%), MODIS tends to have a low bias (0.02–0.03). The agreement between MODIS and AERONET AOD does not depend on MODIS quality assurance confidence (QAC) value. However, when stratified by satellite, MODIS-Terra data does not perform as well as Aqua, with especially poor correlation (r = 0.39) for low aerosol loading conditions (AERONET AOD less than 0.15). Linear regressions between Terra and AERONET possess statistically-different slopes for AOD < 0.15 and AOD ≥ 0.15. AERONET AOD measured only during MODIS overpass hours is highly correlated with daily-averaged AERONET AOD. MODIS monthly-averaged AOD also tracks that of AERONET over the study period. These results indicate that MODIS is sensitive to the day-to-day variability, as well as the annual cycle of AOD over the Appalachian State AERONET site. The complex topography and high seasonality in AOD and vegetation indices allow us to specifically evaluate MODIS dark target algorithm surface albedo and aerosol model assumptions at a regionally-representative SE US mountain site.