AbstractGut microbiomes are diverse ecosystems whose drivers of variation remain largely unknown, especially in time and space. We analysed a dataset with over 900 red squirrel (Tamiasciurus hudsonicus) gut microbiome samples to identify the drivers of gut microbiome composition in this territorial rodent. The large‐scale spatiotemporal replication in the data analysed was an essential component of understanding the assembly of these microbial communities. We identified that the spatial location of the sampled squirrels in their local environment is a key contributor to gut microbial community composition. The non‐core gut microbiome (present in less than 75% of gut microbiome samples) had highly localised spatial patterns throughout different seasons and different study areas in the host squirrel population. The core gut microbiome, on the other hand, showed some spatial patterns, though fewer than in the non‐core gut microbiome. Environmental transmission of microbiota is the likely contributor to the spatiotemporal distribution observed in the North American red squirrel gut microbiome.