In assessing environmental change, butterflies have been proven as replicable indicators of biodiversity and functional integrity that can be monitored at a range of scales. Butterflies have been identified as important bio-indicators for assessing biodiversity and monitoring ecosystem responses to environmental perturbations. The objectives of this study were to determine changes in the butterfly fauna of differing sites in the Sango Bay Area (SBA) and Iriiri (Karamoja) in comparison with data collected 10 years ago, and to investigate the impact of different degrees of habitat disturbance on butterflies. The general butterfly diversity was determined by trapping and sweep netting along transect lines and by random sweeping. The impact of human-induced disturbance was assessed by comparing species richness and composition between the sites and regressing the weighted disturbances against species diversity per site. There was a marked decrease in species diversity and varied species composition between the two studies and between the habitat types. Charcoal burning and grazing had significant negative correlations with diversity within forest sites (r2 = 0.825, P < 0.05), whereas cultivation and tree cutting/logging had significant negative correlations with diversity of open savannas (r2 = 0.718, P < 0.05 and r2 = 0.999, P < 0.05, respectively).