Pneumocystis jirovecii is an opportunistic fungi pathogen that causes pneumocistosis (PCP) in immunocompromised patients. Humans are its only host and it is transmitted among people by aerosols. PCP occurs primarily in hospital settings where it can also cause an outbreak. Genotyping methods are nowadays used for better understanding of the epidemiological characteristics of fungi, particularly multi locus genotyping (MLST). In our study we used clinical samples from patients with PCP and did MLST with five loci: DHPS, ß-tubulin, mt26S rRNA, CYB and SOD. Study included 73 respiratory samples of 53 patients received from January 2012 to December 2014. We managed to successfully genotype 40 samples of 32 patients. We found 15 different sequence types of P. jirovecii which were separated in seven genotype groups. Based on the genotyping results of fungi and epidemiological data that was available on patients we assume that during the years 2012 to 2014 in clinics / hospital wards where we received samples from, there were no outbreaks of PCP. There was only some individual transmissions between patients and to clarify these we would need additional epidemiological data on patients.