Cryptococcosis is a serious disease possessing a wide geographic distribution, with a global burden of 957,900 cases of cryptococcal meningitis per year, resulting in 624,700 deaths. It is an opportunistic mycosis caused by a complex called Cryptococcusneoformans and C. gattii, classifed into four subtypes: VNI-VNII, VNIII, VNIV and VGI, VGII, VGIII, VGIV. It is most critical when it affects immunocompromised patients, with AIDS, tuberculosis or other diseases that require prolonged hospitalization. This study described a molecular epidemiology, the phylogenetic relationship, along with antifungal susceptibility test of a new ST 623 of C. neoformans isolated in a patient with non-Hodgkin's Lymphoma, from Manaus, Brazil. Following the two positives blood cultures, the subculture was carried out in modifed Sabouraud dextrose agar and later in the media of canothothin-glycine blue bromothymol (CGB) and Niger Seed Agar for species diferentiation. The phenotypic identification and minimum inhibitory concentration (MIC) values for fuconazole, amphotericin B and fucytosine were performed using VITEK-2 Compact equipment. DNA was extracted using DNeasy Blood & Tissue Kit according to the manufacturer's instructions. The molecular identification of the fungus was determined applying the enzymatic restriction protocol (PCR–RFLP). Sequences of the MLST genes were compared with other VNI subtypes sequences, selected due to genetic proximity criterion that ST623 has with this group and deposited in the MLST database. The nucleotide sequences were edited and aligned by the MEGA × program using the MUSCLE tool. The alignenment were analysed using MEGA × and DnaSP 6.0 programs. The phylogenetic tree were edited using ITOL program. To reconstruct the phylogenetic relationship between STs and VNI subtypes, the sequence of the seven MLST markers were concatened and analysed to choose the evolutive model ‘Kimura 2 parameters’ for analysis, with gamma distribution and invariable substitution rates. The microbiological test realized identified Cryptococcus neoformans. MIC showed susceptibility to all antifungal tested. PCR-RFLP protocol identified the molecular type VNI, and comparative analyzes with the sequences deposited on the MLST website, made it possible to identify a new clone of Cryptococcus neoformans ST623. GenBank accession numbers of the C. neoformans allele from our case are MN065812, MN065813, MN065814, 217 MN065815, MN065816, MN065817, and MN065818. Our results showed that ST623 new clone has no evident evolutionary proximity to any other ST of the VNI subtype group identified in Brazil. In the evolutionary context of phylogenetic analysis, this new genotype belongs to VNI subtype, and subsequencing complete genome studies are necessary to better understand the phylogenetic relationships amongst STs in this group.