House mice (Mus musculus L.) are known to carry ectoparasites that can cause dermatitis and serve as vectors for human diseases. However, little is known about the prevalence and diversity of ectoparasites on house mice in human apartments. In this study, we collected and identified ectoparasites from house mice trapped in apartment buildings and a chicken breeding facility across three cities in New Jersey, USA. A total of 189 house mice were captured from apartment buildings, while 113 were trapped near the chicken breeding building. Mites were the only ectoparasites detected, with the infestation rates ranging from 25% to 89% across sites. Mite species richness varied from 1.0 ± 0.0 to 2.2 ± 0.1 species per mouse. Four mite species were identified, Myocoptes musculinus (Koch), Myobia murismusculi (Schrank), Echinonyssus butantanensis (Fonseca), and Liponyssoides sanguineus (Hirst), also known as the house mouse mite. In addition, two blood-sucking mite species were genetically barcoded to support future species identification. The house mouse mite was the only medically significant species, found exclusively in apartment buildings, with a prevalence of 30% to 79% and a mean density of 2.6 ± 0.6 to 8.5 ± 1.2 mites per mouse. This study marks the first reports of E. butantanensis and the house mouse mite on house mice in New Jersey. These findings are significant, as the house mouse mite poses a potential health risk to humans in buildings where infestations are common.