Red squirrel populations have declined in the UK since the introduction of the grey squirrel, due to resource competition and grey squirrels carrying a squirrelpox virus that is fatal to red squirrels. It is not known if the gut microbiota of the two species is similar and if this could impact the survival of red squirrels. The aim of this study was to profile the caecal microbiota of red and grey squirrels obtained opportunistically from a conservation programme in North Wales. Bacterial DNA was extracted from ten red and ten grey squirrels and sent for 16S rRNA sequencing. Three samples from red squirrels returned less than 5000 reads, and so were not carried forward for further analyses. Samples taken from the caeca of red squirrels had significantly lower bacterial diversity and a higher percentage of Bacilli bacteria when compared to samples from grey squirrels. When the abundance of bacterial groups across all levels of phylogenetic classifications was compared between the two groups of squirrels, grey squirrels had a higher abundance of bacteria belonging to the families S24-7, RF39 and Rikenellaceae. with resistance to amoxicillin/clavulanic acid was identified in all samples. Cefotaxime resistance was identified in two samples from grey squirrels along with sulfamethoxazole/trimethoprim in one of these samples. Clear differences between the caecal microbiota of the two species of squirrel were identified, which could potentially impact their overall health and ability to compete for resources.