Microbial keratitis is a significant cause of corneal blindness worldwide. Important but frequently misdiagnosed pathogens include Pythium insidiosum, filamentous fungi, and Acanthamoeba species (spp). Their clinical presentations frequently overlap, and delayed or inappropriate treatment can lead to irreversible vision loss. Therefore, understanding the anatomical basis of infection, natural history, and patterns of spread among these entities is crucial for accurate diagnosis and timely management. Please see StatPearls' companion resource, "Pythium Keratitis," for further information. The cornea, a transparent avascular structure composed of 5 layers: the epithelium, Bowman layer, stroma, Descemet membrane, and endothelium, which function as both a refractive medium and a barrier to infection. Microbial invasion typically begins with epithelial defects resulting from trauma, surgery, or contact lens wear, followed by stromal colonization. Differences in organismal biology determine the route of invasion, tissue response, and clinical evolution (Table 1). Pythium insidiosum keratitis is caused by an aquatic oomycete belonging to the kingdom Straminipila that is found in stagnant water, rice paddies, and moist soil. Infection follows corneal inoculation by contaminated water, vegetation, or soil, particularly in humid, tropical environments. The organism produces slender, aseptate filaments that invade the corneal stroma radially, creating a characteristic reticular or tentacular appearance with limited necrosis but extensive enzymatic degradation. The absence of chitin and ergosterol in its cell wall renders antifungal drugs ineffective. Clinically, the disease progresses rapidly within days, causing severe pain, a grayish, dry-looking stromal infiltrate with tentacular projections, and endothelial plaques (See Image. Pathognomic Features of Pythium insidiosum Keratitis). Notably, the lesion may appear deceptively inactive despite aggressive antifungal therapy, a key diagnostic clue. The natural course is fulminant, often requiring early therapeutic keratoplasty to preserve the globe. Fungal keratitis, caused by Fusarium, Aspergillus, Curvularia, or Candida organisms, is more common and relatively more indolent than Pythium keratitis. Trauma with plant material or contact lenses is a typical cause. Septate hyphae invade the anterior and midstroma, resulting in necrosis and feathery-edged infiltrates with satellite lesions. The infection evolves over days to weeks and typically responds to natamycin or voriconazole. The infiltrate appears soft, raised, or fluffy, with surrounding edema; descemetocele formation or perforation occurs late in the disease course. Proper identification via potassium hydroxide preparation or Calcofluor White staining, which highlights septate branching hyphae, enables timely antifungal therapy and improves outcomes. Acanthamoeba keratitis, a parasitic infection caused by Acanthamoeba castellanii and related species, primarily affects contact lens wearers or those exposed to contaminated tap water. The organism adheres to the corneal epithelium through mannose-binding proteins and invades the stroma along corneal nerves. The hallmark feature is perineural inflammation, producing severe pain disproportionate to clinical findings. The disease course is chronic and relapsing, characterized by punctate epithelial erosions progressing to ring infiltrates over weeks. Confocal microscopy reveals double-walled cysts within the stroma. Because of its indolent course, Acanthamoeba keratitis is often misdiagnosed as herpetic or fungal keratitis, leading to delayed diagnosis and prolonged recovery. Table 2 summarizes the distinguishing characteristics of each organism. The pattern of spread and host inflammatory response further differentiates these infections. Pythium spp spreads centrifugally through stromal lamellae to the Descemet membrane and limbus, provoking an intense neutrophilic reaction and tissue melt. Fungal hyphae, in contrast, cause granulomatous or mixed inflammation, progressing slowly through anterior and midstromal planes. Acanthamoeba spp exhibits unique perineural spread, resulting in radial keratoneuritis and a ring-shaped infiltrate with a lymphocytic host response. Table 3 summarizes the patterns and characteristics of dissemination. Abbreviations: GMS, Grocott-Gomori methenamine silver (stain); PAS, periodic acid Schiff (test); TPK, therapeutic keratoplasty. Diagnostic differentiation among the 3 conditions is notoriously difficult. P insidiosum is often mistaken for filamentous fungal keratitis on smears because of its filamentous morphology. Acanthamoebae cysts may be missed on routine staining unless special techniques such as Calcofluor White or periodic acid-Schiff (PAS) are used. Advanced diagnostic tools such as confocal microscopy, polymerase chain reaction (PCR), and culture on blood agar (for Pythium spp) or nonnutrient agar (for Acanthamoeba spp) enhance specificity. Recently, artificial intelligence (AI)-based diagnostic models using slit-lamp and smartphone images have achieved greater than 90% accuracy in differentiating Pythium keratitis from fungal keratitis, offering promise for point-of-care screening in low-resource regions. In summary, Pythium keratitis is an acute, aggressive, antifungal-resistant infection characterized by a reticular tentacular infiltrate. In contrast, fungal keratitis has a more indolent course, with fluffy, feathery margins that respond to antifungals. Acanthamoeba keratitis is characterized by a chronic, painful, ring-shaped infiltrate and cystic pathology. Recognizing these distinctions, supported by confocal imaging, microbiology, and AI-driven diagnostics, is vital for appropriate management and visual prognosis. Please see StatPearls' companion resource, "Corneal Ulcer," for further information.