In this chapter, we consider some of the “root-infecting” pathogens of Theobroma cacao. Despite sometimes being described as minor pathogens of the crop, they can cause serious losses locally. We have chosen to examine four pathogens—Verticillium dahliae (Verticillium wilt or sudden death), Rigidoporus microporus (white root disease), Rosellinia spp. (black rot), and Phellinus noxious (brown root rot). These are all soil-borne, root-infecting fungi, but whilst the basidiomycetes and Rosellinia (ascomycete) are unspecialized, opportunistic root rot pathogens whose pathogenicity is part of a saprophytic lifestyle, Verticillium is a highly specialized pathogen adapted for colonization of the xylem system. Yet, despite differences in their pathogenicity, there are some important practical similarities with regard to their management. These pathogens are extremely difficult to manage given their soil-borne nature, colonization of alternative hosts and/or colonization of woody debris, and the perennial nature of the cacao host plant. Currently, cultural methods are often used as the main management approaches with chemical control being considered too costly or ineffective. Development of breeding programs against the unspecialized pathogens is one area of research that should be expanded; successful breeding programs have been undertaken for Verticillium in Brazil. Biological control is another area where further work is needed for all these pathogens both with regard to the direct application of biological control agents (BCAs) themselves and on the interaction with BCAs and various soil amendments to enhance naturally occurring antagonists. There may be differences in approach here based on modes of pathogenicity, but inevitably, we should be aiming at an integrated approach for these pathogens.