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<i>Mycoplasma</i> spp. pathogens frequently cause chronic and acute diseases in cats. The aim of the present study was to investigate the presence and genetic diversity of <i>Mycoplasma</i> spp. in cats and their ectoparasites using PCR and sequence analysis of the <i>16S rRNA</i> gene. Blood samples were collected from 541 domestic and stray cats in Lithuania. Ectoparasites (153 fleas and 321 ticks) were collected from owned domestic cats that live both outdoors and indoors. <i>Mycoplasma</i> spp. were detected in 7.2% of cat blood samples and 4.4% of <i>Ctenocephalides felis</i> fleas. The sequence analysis revealed the presence of <i>Mycoplasma haemofelis</i> in 1.1% of cats and ‘<i>Candidatus</i> Mycoplasma haematominutum’ in 4.8% of cats. <i>Ct. felis</i> fleas harboured <i>M. haemofelis</i>. To the best of the authors’ knowledge, this is the first report on the prevalence and molecular characterisation of <i>Mycoplasma</i> bacteria in cats in Lithuania and cat fleas in the Baltic States.