The aphotic formation of natural organohalogens (NOHs) remains inadequately understood, in contrast to the well-documented photo-halogenation process of dissolved organic matter (DOM), despite the significant biogeochemical implications associated with NOHs. This study investigates the differences in the formation of chlorinated and brominated compounds from the photochemical and aphotic reactions of native Phragmites australis (PA-DOM) and invasive Spartina alterniflora (SA-DOM). The findings indicate that SA-DOM exhibits a greater potential for photochemical halogenation, attributed to its higher aromatic content and enhanced photostability. Utilizing advanced mass spectrometry, the study identifies nitrogen-containing and free saturated compounds as primary precursors for both types of DOM during photochemical halogenation. Notably, significant disparities in the halogenation processes of lignin/CRAM, nitrogen-containing/free saturated compounds, and amino sugars between SA-DOM and PA-DOM are observed, leading to a higher production of NOHs in PA-DOM during aphotic reactions compared to photic reactions, even in artificial seawater. Furthermore, the study emphasizes the critical role of dissolved oxygen in the formation of NOHs from PA-DOM under aphotic conditions. Given the rapid fluctuations in oxygen levels, salinity, and solar intensity, alongside tidal and diurnal cycles, the significance of both photic and aphotic pathways for NOHs formation should not be overlooked.