For decades, parasitic worms such as Trichuris muris have been maintained in laboratory animals, providing insights into host–parasite interactions and host immune responses. The most used T. muris isolate is the E isolate, established in the laboratory in 1954. However, one concern with these model systems is the potential for laboratory‐induced selection and therefore changes in host–parasite interactions. To address these concerns, we compare the E isolate with a recently isolated T. muris isolate (M isolate), established from wild house mice (Mus musculus domesticus, Isle of May, UK), in their capacity to infect laboratory mice. High dose infection of C57BL/6 mice revealed that significantly more parasites of the M isolate survived to the adult stage compared to the E isolate. Worm persistence was associated with heightened TNF‐α and IL‐10 secretion upon parasite‐specific re‐stimulation, and higher serum IgG1 and IgG2c levels, concomitant with an increase in T‐bet+ and ICOS+ CD4+ T effector‐memory cells. Differences in host response to the isolates were not as pronounced during low dose infection. Our study highlights the need for regular evaluation of lab‐maintained parasite isolates against freshly isolated parasites to understand whether the established lab strains remain relevant model systems for our understanding of parasitic infections.