Boron-resistant fungi were isolated from the wastewater of a boron mine in Turkey. Boron removal efficiencies of Penicillium crustosum and Rhodotorula mucilaginosa were detected in different media compositions. Minimal Salt Medium (MSM) and two different waste media containing molasses (WM-1) or whey + molasses (WM-2) were tested to make this process cost effective when scaled up. Both isolates achieved high boron removal yields at the highest boron concentrations tested in MSM and WM-1. The maximum boron removal yield by P. crustosum was 45.68% at 33.95 mg l−1 initial boron concentration in MSM, and was 38.97% at 42.76 mg l−1 boron for R. mucilaginosa, which seemed to offer an economically feasible method of removing boron from the effluents.