In eukaryotic cells, large GTPases of the dynamin superfamily are important drivers of membrane curvature and constriction during membrane fusion and fission processes. We have identified a family of dynamin-like proteins in pathogenic bacteria, such as the gastric carcinogen H. pylori and enterotoxigenic Escherichia coli. In this family, one of the dynamin genes is split into two ORFs (named dlp1a and dlp1b in H. pylori), which are upstream of another full-length dynamin gene dlp2. Interestingly, we identified a single-nucleotide indel in a region of overlap in dlp1a and dlp1b that differs between sub-isolates of H. pylori, leading to either the split or the joined forms of dlp1 (the full-length gene). Analyses of dlp1 and dlp2 mRNA and their protein products were consistent with this genotypic variation, and might represent a novel regulation mechanism. The gene arrangement and presence of a predicted transmembrane helix in Dlp1b, similar to the membrane-binding domain of eukaryotic dynamin, suggests that these proteins might act as a hetero-complex involved in bacterial membrane dynamics. In strains containing the fused dlp1, western blotting and immuno-fluorescence microscopy suggested that Dlp1 is membrane-associated, whereas Dlp2 is approximately equally distributed between the cytosol and membrane. Knock-out of the dlp operon caused a high proportion of cells to develop a compromised cell membrane in dye-penetration assays, and minimal growth in acidic conditions. Quantitative proteomics of the acid response in wild-type and knock-out strains has further highlighted the potential role dynamins have in acid adaptation. As acid tolerance is essential for H. pylori during colonization of the stomach, our results suggest that the H. pylori dynamin-like proteins are important in establishing H. pylori infections, which affect over half the world’s population.