We evaluated the diagnostic performance of the newly developed MoiM Dx Candida 9-plex (MoiM) assay for the detection of Candida species from positive blood cultures and compared the results with those obtained from the BIOFIRE Blood Culture Identification 2 (BCID2) Panel. This study included 39 candidaemia cases and 40 cases of non-Candida bloodstream infections as negative controls. Routine culture results, which were identified via matrix-assisted laser desorption/ionization time‒of‒flight mass spectrometry (MALDI‒TOF MS), were used as the reference standard for analysis. The performance of the MoiM assay was evaluated using positive percent agreement (PPA) and negative percent agreement (NPA). The MoiM assay demonstrated a PPA of 97.1% and an NPA of 100% for detecting the five most common Candida species (C. albicans, C. glabrata, C. tropicalis, C. parapsilosis, and C. krusei) in candidaemia cases. In comparison, the BCID2 panel yielded a PPA of 67.6% and an NPA of 100.0% (P = 0.001). Additionally, the MoiM assay correctly identified C. guilliermondii and C. lusitaniae, not covered by the BCID2 panel. Among the 10 discrepant results between the two assays, all 10 cases were incompletely identified by the BCID2 panel, but the results from the MoiM assay were identical to the culture results. The MoiM assay was designed as an automated sample-to-answer molecular assay for the detection of Candida species from positive blood cultures. Our study revealed that this assay shows good overall agreement with routine culture and is comparable to the BCID2 panel.