<p>The small mammal gut microbiome can affect wildlife physiology and microbial dispersal. Composition of this microbiome can be influenced by habitat characteristics and host species, yet the effects of habitat management, such as restoration, are still largely unknown. In this study, our goal was to identify the influence of 1) small mammal host species and 2) longleaf pine (<i>Pinus palustris</i>) habitat restoration phase on the fungal and bacterial communities within small mammals’ gut microbiomes. During the falls of 2023 and 2024, we trapped small mammals and collected their scats at 6 sites in Florida, USA. Sites were categorized into unrestored pine plantation (<i>n</i> = 2) and late-phase restoration (restored &gt; 18&#xa0;years prior; <i>n</i> = 4). Notably, our capture rates were very low with 0.0077 and 0.0034 captures/trap night in 2023 and 2024, respectively. We observed that the bacterial gut microbiome varied by host species (i.e., oldfield mouse [<i>Peromyscus polionotus</i>] versus hispid cotton rat [<i>Sigmodon hispidus</i>]), whereas the fungal gut microbiome varied by habitat restoration phase (i.e., late-phase restoration versus unrestored pine plantations). Overall, this study is the first to examine small mammal microbiomes in longleaf pine savannas and thus provides baseline insights into the interactions between small mammals and microbes associated with this ecosystem.</p>