Fungal keratitis is a severe infection that often requires surgical intervention and is associated with poor outcomes. Penetrating keratoplasty allows for the complete removal of the fungal infiltrate and thus can be a turning point in therapy. The depth of pathogen invasion, which cannot always be reliably assessed by slit lamp examination, can be accurately determined through histological analysis of the corneal trephinate. In this study, we histologically analyzed two corneal trephinates obtained during an emergency keratoplasty performed for uncontrollable mycotic infections. In case 1, caused by Candida albicans, the infiltrate remained localized at the site of pathogen entry. In contrast, in case 2, Fusarium falciforme demonstrated extensive tissue invasion, spreading destructively throughout the cornea. This invasion pattern suggests that Fusarium keratitis is difficult to control due to its aggressive spreading behavior within the tissue. This explains the high rate of penetrating keratoplasty required in such cases.