The identification of yeast and yeastlike organisms in tissue sections can be very difficult. Biopsy tissues may be limited, with only occasional organisms present. In addition, several common species have overlapping histologic features. Deoxyribonucleic acid probes were designed to detect both the 18S and 28S ribosomal ribonucleic acid sequences of five fungal organisms with a high degree of specificity for each fungus. Each of these organisms—Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum,andSporothrix schenckii—can be manifested histologically as round, yeastlike structures, often within a similar size range. Probes were tested against 98 archived, formalin-fixed, paraffin-embedded tissue specimens, each of which had culture-proved involvement by one of these organisms. Assessment of accuracy was based on the presence of yeastlike organisms in consecutive Grocott's methanemine silver (GMS)-stained tissue sections, and agreement with culture results. The results indicated that GMS had a greater overall sensitivity in detecting fungal organisms (95.9%) compared with in situ hybridization (ISH; 82.7%). ISH with oligonucleotide deoxyribonucleic acid probes, however, was more specific, with all species-specific probes yielding 100% specificity (compared with 96.2–100% specificity based on morphology alone). ISH also had a higher positive predictive value (100% in all cases) compared with GMS (83.3–100%). In addition, four cases with rare organisms present (4.1% of cases tested) were detected by ISH but not by GMS staining. These results show that ISH, directed against ribosomal ribonucleic acid, provides a rapid, accurate technique for the identification of yeastlike organisms in histologic tissue sections. Its primary strength lies in the ability to speciate organisms accurately that are too few or atypical to identify based solely on morphologic features.