The rising incidence of fungal infections coupled with limited treatment options underscores the urgent need for novel antifungal therapies. Riboswitches, particularly thiamin pyrophosphate (TPP) class, have emerged as promising antimicrobial targets. This study presents a comprehensive genome-wide analysis of TPP riboswitches in 156 medically relevant fungi utilizing advanced covariance models (CMs) tailored for fungal sequences. Our investigation identified 378 conserved TPP riboswitch sequences distributed across 140 distinct species, revealing a broader prevalence than that previously recognized. Notably, we provide evidence for a novel putative group of TPP riboswitches, designated TPPswˢᵁᴳᴬᴿ, associated with sugar transporters in Mucoromycota and Basidiomycota. This group exhibits distinctive structural features while maintaining key TPP-binding motifs, potentially expanding our understanding of the riboswitch diversity in fungi. Our analysis highlights the impact of P3 stem variability on riboswitch detection and characterization, demonstrating the superiority of fungal-specific CMs over generic models. We observed multiple TPP riboswitches in over 50% of the examined species, including clinically significant pathogens involved in aspergillosis and mucormycosis. Remarkably, Aspergillus latus, a species associated with COVID-19 coinfections, harbors six distinct TPP riboswitch sequences, whereas the extremophilic black fungus Hortaea werneckii possesses nine. These findings not only elucidate the diverse distribution of TPP riboswitches in pathogenic fungi but also emphasize their potential as multifaceted targets for antifungal drug development. By addressing key limitations of previous detection methods and providing insights into riboswitch structural diversity, this study lays a foundation for future investigations into riboswitch-mediated regulation in fungi and the development of novel antifungal strategies.