Background: Present study deals with the removal of Zn(II) ions from effluent using yeast biofilm formed on gravels. Methods: The biofilm forming ability of Candida rugosa and Cryptococcus laurentii was evaluated using XTT (2,3-bis [2-methoxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide) reduction assay and monitored by scanning electron microscopy (SEM) and Confocal laser scanning microscopy (CLSM). Copious amount of extracellular polymeric substances (EPS) produced by yeast species was quantified and characterized by Fourier transform infrared spectroscopy (FT-IR). Results: Yeast biofilm formed on gravels by C. rugosa and C. laurentii showed 88{\%} and 74.2{\%} removal of Zn(II) ions respectively in batch mode. In column mode, removal of Zn(II) ions from real effluent was found to be 95.29{\%} by C. rugosa biofilm formed on gravels. Conclusion: The results of the present study showed that there is a scope to develop a cost effective method for the efficient removal of Zn(II) from effluent using gravels coated with yeast biofilm. {\textcopyright} 2014 Basak et al.; licensee BioMed Central Ltd.