Extremely low-frequency electromagnetic fields (ELF-EMF) and radiofrequency electromagnetic fields (RF-EMF) have been considered to be possibly carcinogenic to humans. However, their genotoxic effects remain controversial. To make experiments controllable and results comparable, we standardized exposure conditions and explored the potential genotoxicity of 50 Hz ELF-EMF and 1800 MHz RF-EMF. A mouse spermatocyte-derived GC-2 cell line was intermittently (5 min on and 10 min off) exposed to 50 Hz ELF-EMF at an intensity of 1, 2 or 3 mT or to RF-EMF in GSM-Talk mode at the specific absorption rates (SAR) of 1, 2 or 4 W/kg. After exposure for 24 h, we found that neither ELF-EMF nor RF-EMF affected cell viability using Cell Counting Kit-8. Through the use of an alkaline comet assay and immunofluorescence against γ-H2AX foci, we found that ELF-EMF exposure resulted in a significant increase of DNA strand breaks at 3 mT, whereas RF-EMF exposure had insufficient energy to induce such effects. Using a formamidopyrimidine DNA glycosylase (FPG)-modified alkaline comet assay, we observed that RF-EMF exposure significantly induced oxidative DNA base damage at a SAR value of 4 W/kg, whereas ELF-EMF exposure did not. Our results suggest that both ELF-EMF and RF-EMF under the same experimental conditions may produce genotoxicity at relative high intensities, but they create different patterns of DNA damage. Therefore, the potential mechanisms underlying the genotoxicity of different frequency electromagnetic fields may be different.