Most organisms have a resident microbial community (microbiome) associated with them. The importance of these communities to the health and overall functioning of their hosts is becoming increasingly recognized. New advances in sequencing technology have made it possible to examine marine microbial diversity more fully. Because bacteria play such important roles in the ecology of marine organisms and because their abundance is so high in seawater, it is likely that marine organisms have evolved mechanisms to regulate the bacterial community surrounding them. There is growing evidence that many marine organisms host species-specific bacterial communities on their surfaces and/or within their tissues/bodies. This chapter discusses what is known about the role of secondary metabolites in the negative (i.e., chemical defenses) and positive (i.e., microbiome formation) regulation of macroalgal-associated microbial communities within benthic marine environments. The final section reviews the effects of algal metabolites on the microbial communities of near neighbors—a new concentration in marine microbial defenses.