In order to suppress the growth of Pseudo-Nitzschia sicula and N. frustulum appearing during the cultivation of filaments of Scytosiphon lomentaria in our lab, the effects of germanium dioxide (GeO₂) at 1.00−4.00 μg/mL on the growth and development of filaments of S. lomentaria and the growth of epiphytic diatoms were studied in 3 different kinds of co-cultured systems. Results indicated that: ① the suitable concentrations of GeO₂ for co-cultured systems of filaments and diatoms were 1.00−2.50 μg/mL, at which the percentage decreases of diatoms were all above 67.33%±5.18% after 14-day co-culturing, meanwhile the filaments of S. lomentaria were in good conditions and good developments. 2.00 μg/mL was the most suitable concentration of GeO₂ since the filaments of S. lomentaria, under that condition, had the highest daily average growth rates which were all higher than 11.00% in 3 kinds of co-cultured systems, and ratios of sporangial branchlets as well as average diameter of sporangia were 57.47%±5.31% and (24.55±1.01) μm, respectively, which were not significantly different from those in control groups. ② Although diatoms were suppressed more effectively when the concentrations of GeO₂ was up to 3.50 and 4.00 μg/mL, the growth of filaments, the ratios of sporangial branchlets and average diameter of sporangia after inducing were also influenced negatively. What is more, filaments were dead when the concentration of GeO₂ reached 4.00 μg/mL. ③ N. frustulum is more sensitive to GeO₂ than P. sicula. After 14-day co-culturing, the percentage decreases of N. frustulum were between (82.10%±2.40%)−(96.35%±0.79%) at any concentration of GeO₂, which were higher than the percentage decreases of P. sicula under same conditions. Moreover, on the 14th day in co-cultured systems of filaments of S. lomentaria, P. sicula and N. frustulum, there was negative correlation between percentages of N. frustulum in the two species of diatoms and concentrations of GeO₂.