Fungal chitosan (ACT) extraction from Amylomyces rouxii, its transforming into nano-form, loading with fluconazole (Flu) and evaluation of synthesized nanoconjugates against drug-resistant (DR) Candida spp., were investigated. The produced ACT was characterized with 112.4 kDa molecular weight and 88.7% deacetylation degree. Synthesis of chitosan nanoparticles (NACT), and loading them with Flu were succeeded, using ionic gelation protocol, to generate stable Flu/NACT nanoconjugate' particles with mean size of 82 nm and zeta potential of +3.36 mV. The NACT entrapment efficiency was 78.7% and the drug loading capacity was 60.2%. Flu slowly released from NACT during the first 5 h, then release dramatically increased to the maximum (94.8%) after 12 h. The infra-red spectrum of Flu/NACT nanoconjugates confirmed the strong cross-linkage between their molecules. The antimycotic activity of NACT and Flu/NACT was proved against DR strains of C. albicans (2 strains), C. parapsilosis and C. glabrata, using qualitative and quantitative assays; Flu/NACT exhibited significant powerful activity, which was confirmed via observations with scanning microscopy. Finished cotton textiles with Flu/NACT had augmented potentiality for inhibiting challenged DR Candida spp., using in vitro assay. Accordingly, the synthesis and application of Flu/NACT nanoconjugates was astoundingly recommended for controlling DR Candida spp.