Recently, there has been a lot of interest in the synthesis and application of nanoparticles with anisotropic morphologies. The focus of this study has been to use a biologically mediated, low temperature approach for the synthesis of zinc oxide nanoflowers. “Green” methods have a number of advantages over conventional approaches; these include the use of environmentally benign reactants and its economic feasibility. The cell free extract of Chlamydomonas reinhardtii, a fresh water microalga was used to synthesize the nanoflowers. The nanoflowers were composed of individual nanorods that assembled to form flower‐like structures. The nanorods measured 330 nm in length and these nanorods self‐assembled to form porous nanosheets that were found to measure 55–80 nm. Particle size analysis revealed that the larger porous nanoflowers approximately measured 4 µm. Powder X‐ray diffraction studies revealed that the zinc oxide nanoflowers had a hexagonal wurtzite crystal structure. Fourier transform infrared spectroscopy analysis suggested that algal biomolecules were responsible for the synthesis and stabilization of zinc oxide nanostructures. These nanoflowers demonstrate enhanced photocatalytic activity against methyl orange (MO) under natural sunlight. The effects of dye concentration and catalyst dosage on photocatalysis were also studied. The present approach represents a novel, eco‐friendly method to synthesize zinc oxide nanoflowers that have potential applications in water treatment and dye degradation. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 1020–1026, 2016