Fluorescence imaging has emerged as a transformative tool in parasitological research, providing high-contrast visualization of complex morphologies often obscured in traditional bright-field microscopy. This review article synthesizes recent advancements in the application of polycyclic aromatic fluorophores, specifically benzanthrone and anthraquinone derivatives, for helminth imaging. It evaluates the critical interplay between chemical fixation strategies, such as ethanol-based protein precipitation, and optical clearing agents like ethanol–xylene and lactic acid to optimize tissue transparency for confocal laser scanning microscopy. Recent practical applications are examined across diverse taxa, demonstrating that the rational design of N-substituted sensors—including aminoamides and aminophosphonates—enables high-resolution characterization of muscular–tegumental systems and reproductive organs in under one hour. Key breakthroughs highlighted include the rapid sex determination of Trichinella larvae and the detailed resolution of the tripartite muscle framework in trematodes like Prosotocus confusus. These developments establish anthrone-based sensors as a robust, efficient alternative to conventional commercial kits, offering superior photostability and spectral tunability.