Technical Abstract: As humic substances represent relatively high molecular mass polyelectrolytes containing aromatic, aliphatic and heterocyclic subunits, capillary electrophoresis (CE) has become an attractive method for “finger-print” characterization of humic acids. In addition, fluorescence excitation-emission matrix (EEM) spectroscopy is also a highly sensitive analytical method, providing information on flurophore properties of humic acids. However, basic information on the CE profile patterns and fluorophore components of humic acid fractions from different agricultural soils is rare. Consequently, we sequentially extracted the mobile humic acid (MHA) and recalcitrant Ca humate (CaHA) fractions from Nebraska corn soils and Philippine rice soils under different fertilization schemes, and acquired their CE profiles and fluorophore component composition. We observed greater differences in the CE profiles between soils than between management practices on the same soil, reflecting the distinct “finger-print” CE features of these soil humic fractions. Modeling analysis of EEM data indicated that four fluorophore components were present in these humic fractions. Whereas three have previously been reported in literature, we propose the features of the unknown component as being relevant to agricultural humic fractions. UV irradiation seemed to impact the Nebraska soils by disaggregating the humic fractions into their structural subunits, while impacting the Philippine soils by altering the functional groups of humic fractions. This research provides insight into the CE profiles and fluorophore features of humic acid fractions from different agricultural soils.