Targeting the control of pathogenic Candida spp., especially the fungicides resistant strains from C albicans and C glabrata, nanoconjugates from the biopolymer (chitosan) and costus root extract (Saussurea costus) was synthesized and characterized. Chitosan was extracted from the grown mycelia of Aspergillus niger and characterized with high deacetylation degree of 91.2% and moderate molecular weight of 106.8 kDa. Synthesis of nanoconjugates from fungal chitosan/costus extract (NCt/CE) was conducted using ionic gelation technique; the resulted NCt/CE particles were characterized with mean diameter of 48 nm, positive zeta potentiality (+3.28 mV) and high stability. The infra‐red spectra of synthesized nanoconjugates indicated their strong biochemical cross‐linkage. The antimycotic activities, of the synthesized NCt, CE and their nanocomposite, were evaluated against standard and antibiotic‐resistant strains from C albicans and C. glabrata and revealed that the entire agents had notable antimycotic potentiality against all examined strains; the NCt/CE nanoconjugates had significantly stronger antimicrobial action. The scanning microscope imaging, of exposed resistant strains to NCt/CE, indicated their vigorous structural and morphological alterations and confirmed the antimycotic activity of the nanocomposite. NCt/CE nanoconjugates' synthesis could be exceedingly recommended as a natural, biodegradable and effectual antimycotic agent to control resistant pathogenic yeast strains.