The periphytic green alga Cladophora glomerata is found growing abundantly in dense mats in lakes and rivers worldwide, often co-occurring in eutrophic lakes with near-shore waters saturated in methane. This alga hosts a diverse microbial community, but the spatiotemporal dynamics of the alga’s bacterial microbiota over a growth season have not been characterized. In this study, replicate samples of Cladophora were collected in 2014 from multiple locales in Lake Mendota at multiple times during the summer growth season to test the hypothesis that the bacterial community changes over time and is geographically heterogeneous. These sequences were amplified from epibiontic bacteria using the 16S rDNA biomarker.