The aim of this study was to test three flat plate photobioreactor configurations for growth of Chlorella vulgaris under non-axenic conditions and to characterize and quantify associated bacterial communities. The photobioreactor cultivations were conducted using tap water-based media to introduce background bacterial population. Growth of algae was monitored over time with three independent methods. Additionally, the quantity and quality of eukaryotes and bacteria were analysed using culture-independent molecular tools based on denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative polymerase chain reaction (QPCR). Static mixers used in the flat plate photobioreactors did not generally enhance the growth at the low light intensities used. The maximum biomass concentration and maximum specific growth rate were 1.0 g l−1 and 2.0 day−1 respectively. Bacterial growth as determined by QPCR was associated with the growth of C. vulgaris. Based on PCR-DGGE, bacteria in the cultures mainly originated from the tap water. Bacterial community profiles were diverse but reproducible in all flat plate cultures. Most prominent bacteria in the C. vulgaris cultures belonged to the class Alphaproteobacteria and especially to the genus Sphingomonas. Analysis of the diversity of non-photosynthetic microorganisms in algal mass cultures can provide useful information on the public health aspects and unravel community interactions.