Ringworm (dermatophytosis) is a fungal infection primarily caused by species in the genus Trichophyton. This disease is highly contagious and capable of spreading through skin-to-skin contact. Importantly, ringworm caused by Trichophyton is a zoonotic disease, capable of spreading between animals and humans. Guinea pigs are a common animal host of Trichophyton species. Although commonly asymptomatic, guinea pigs that present with ringworm can suffer from itchy scabs and alopecia. Ringworm may also weaken the skin and immune systems of guinea pigs, facilitating vulnerability to more serious secondary infections, including antibiotic resistant bacteria such as staphylococci. This study utilized Next Generation Sequencing (NGS) to identify Trichophyton species that could be attributed to ringworm infection and analyzed the guinea pig microbiomes associated with ringworm across 248 samples (234 uninfected vs. 14 infected). The symptoms and microbial pathogens associated with Trichophyton infection in guinea pigs were also reported. This analysis was the first to examine the fungal and bacterial infections associated with ringworm in guinea pigs. Findings from this study substantiate the utility of NGS as a powerful tool for identifying Trichophyton species responsible for ringworm infections.