The complex depositional environment of the Eocene Yegua formation (Brazos County, Texas) can be better understood by integrating organic matter (OM) geochemistry with stratigraphy. Yegua sediments represent parasequences separated by exposure surfaces. Organic petrography and geochemistry (biomarkers, C/N ratios, and carbon isotopes) indicate the presence of both terrestrial and marine OM in transgressive sediments. In contrast, regressive sediments contain only terrestrial OM. These differences relate to contrasting OM sources and depositional styles on the shelf. OM in the sediments is immature and the potential for generating hydrocarbons is poor. The study suggests that organic geochemical data can help in distinguishing transgressive and regressive environments in sedimentary formations.