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The objective of this study was to evaluate the effects of nanoparticles (nanospheres and nanocapsules) of the promising antifungal 2-amino-thiophene (6CN10) and 6CN10 complexed with 2-hydroxypropyl-β-cyclodextrin (6CN10:HP-β-CD) in vitro and compared with free drug against Candida and Cryptococcus, using a microdilution method to measure susceptibility. The Candida and Cryptococcus clinical strains were identified using phenotypic methods and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). To measure in vitro antifungal susceptibility, we used microdilution trials. Serial drug or nanoparticle dilutions were prepared according to the CLSI M27-A3 guidelines. Anti-biofilm activity was verified for Cryptococcus neoformans. All Candida isolates were sensitive to the free drug (MIC = 41.66-333.33 μg/mL) and were able to grow even at the higher concentration tested for all 6CN10 nanoparticles. However, the Cryptococcus neoformans strains presented MIC values of 0.32-83.33 μg/mL for 6CN10 nanoparticles, and MIC values of 0.1-0.2 μg/mL for 6CN10:HP-β-CD nanoparticles, i.e., 3333 times more active than the free drug (MIC values 166.66-333.33 μg/mL), and presenting activity greater than that of the reference drug amphotericin B (MIC = 0.5-0.125 μg/mL). 6CN10:HP-β-CD nanosphere also showed high anti-biofilm potential. The in vitro study showed that the nanoparticles allowed better drug efficiency against Cryptococcus than did the free drug. These results suggest that 6CN10-loaded nanoparticles may become a future alternative for cryptococcosis and candidiasis therapy. In vivo experiments are essential prior to clinical use.