Saproxylic insect communities inhabiting tree hollows in Mediterranean forests depend on a combination of physical characteristics and interactions occurring between community member species. Despite the need to preserve these organisms, little is known about their interrelationships, in particular those relationships between saproxylic insects and microbiota occurring in these microhabitats. In tree hollows of Quercus rotundifolia Lamark that hold water and contain dead leaves, abundant microbial populations can be found. Developing on them are the larvae of Mallota dusmeti Andréu, 1926 (Diptera: Syrphidae), a vulnerable species (IUCN category: Marcos-García and Quinto 2011). This study provides the first data on the microbiota living inside the gut of the larvae of M. dusmeti, as well as the microbiota in the hollow where these larvae develop. Bacteria were identified by amplification and partial sequencing of the V1–V3 regions and the complete nucleotide sequence of 16S rRNA genes. We found eight species of bacteria living in tree hollows and three species in the gut of M. dusmeti larvae: Bacillus cereus, Bacillus toyonensis, and Lysinibacillus sphaericus. The filter-feeding mechanism characteristic of M. dusmeti larvae is selective in enabling ingestion of bacteria only above 2.1 µm in diameter.