The authors report a case of an immunocompetent 38-year-old male who presented with an indolent keratitis that eluded diagnosis after multiple cultures taken over 9 months. He was started initially on medications against Acanthamoeba, after presenting with a nearly complete corneal ring 2 months after trauma. These medications likely partially treated his condition, thereby making laboratory diagnosis more difficult. He was identified as having Encephalitozoon hellum by PCR. The patient subsequently underwent cornea transplant after a full course of medical treatment and recovered best-corrected visual acuity of 20/20.