Macroalgal microbiomes are receiving deserved study, but there is little information about microbial spatial diversity across tissues. Reliance on field material makes it difficult to discern whether recovered microbiomes belong to the host or its epiphytes, and technical comparisons of macroalgal samples for microbial studies are needed. Here, we use a common garden approach that avoids the problem of epiphytes, particularly at holdfasts, to examine the microbiome of Porphyra umbilicalis (strain Pum1). In a second study, we tested whether abiotic stressors that shape the distribution patterns of host macroalgae also affect the composition and structure of their microbiomes using a transplant experiment of three Fucus congeners (F. spiralis, high zone F. vesiculosus, mid zone F. distichus, low zone) during summer in Maine.