The invention features compositions and methods for the detection of Candida species in biological samples, such as human tissue samples. The invention features species specific nucleic acid probes that can hybridize to target nucleic acid molecules in Candida species and can be used in a variety of detection assays, such as fluorescence based assays or NMR based assays. The compositions and methods of the invention can be used to rapidly and accurately detect one or more Candida species in patients and can be used to assist in point-of care-decisions for treating Candida infections.