In the current study, bioremediation of Cu(II) by thermophile Cyanobacterium aponinum has been studied in BG11 media under different conditions. The optimum pH was 9 due to the maximum Cu(II) bioremoval efficiency as 71% in the medium with12.8 mg/L Cu(II). According to the results obtained from the trials, the highest bioremoval was 76.6% in the medium including 9.7 mg/L Cu(II) for incubation period of 10 days. When the effect of increasing temperature (25-45 °C) and biomass [20% and 40% (v/v)] concentrations on bioremediation by C. aponinum was investigated, the highest heavy metal removal was found 75.8% at 45 °C, 12.8 mg/L Cu(II), and 20% (v/v) biomass concentration. It was 76.3% in the medium with 13.8 mg/L pollutant, 40% (v/v) biomass concentration. The qm (maximum specific Cu(II) removal) was found as 6.1 mg/g at 45 °C in BG11 with 40% (v/v) biomass and 13.8 mg/L Cu(II). It has been concluded that Cu(II) bioremediation by thermophile C. aponinum was firstly investigated at various environmental conditions in this study. The results indicated that the tested cyanobacterium had a great potential to remove heavy metals from the aquatic environments, containing Cu(II).