Cryptococcus neoformans consists of two varieties and is divided into five serotypes: serotypes A, D and AD (C. neoformans var. neoformans) and serotypes B and C (C. neoformans var. gattii). This article deals with the investigation on the serotype of C. neoformans by molecular analysis technique in place of the immunological method with antisera against the capsule component of the yeast. For easier and more precise epidemiological surveillance, twenty-seven isolates of C. neoformans were molecularly analyzed by a RAPD method. This method differentiated these isolates of C. neoformans into 4 groups corresponding to the serotypes A, D, AD and complex of serotypes B and C. These results indicated that serotype A, D and AD could be differentiated by the molecular analysis technique described here. Furthermore, nucleotide sequences of CAP59 genes from five serotypes of C. neoformans were analyzed for their phylogenetic relationship. Approximately 600-hp genomic DNA fragments of the CAP59 gene were amplified from each isolate by PCR and sequenced. The CAP59 nucleotide sequences of C. neoformans showed more than 90% similarity among the five serotypes. The phylogenetic analysis of their sequences was divided into three clusters: serotype A and AD, serotype B and C, and serotype D. These results also indicated that serotype B and C isolates belonging to var. gattii were genetically homogeneous and closely related.