Type III secretion systems are used by bacteria for infecting or delivering toxins to eukaryotic or prokaryotic cells. The Gram-negative bacterial flagellum is a type III secretion system, used to secrete proteins in a stepwise, controlled manner to create a motility organelle. Intracellular endosymbionts have been observed to use type III secretion systems to mediate interactions with their hosts. Buchnera aphidicola is an intracellular bacterial symbiont of aphids and maintains a small genome of only 600 kbps. Buchnera is no longer capable of life outside its host. Buchnera is thought to maintain only genes relevant to the symbiosis with its aphid host. Curiously, the Buchnera genome contains gene clusters coding for flagella basal body structural proteins and for flagella type III export machinery. These structures have been shown to be highly expressed and present in large numbers on Buchnera cells. No recognizable pathogenicity factors or secreted proteins have been identified in the Buchnera genome, and the relevance of this protein complex to the symbiosis is unknown. Here we show isolation of the Buchnera flagella from the cellular membrane of Buchnera, confirming the enrichment of flagella proteins relative to other proteins in the Buchnera proteome. This will facilitate studies of the structure and function of the Buchnera flagellar structure, and its role in this model symbiosis.