In this study the prevalence of Methicillin-resistant Staphylococcus pseudintermedius (MRSP) in clinical specimens of different animal species was defined by investigating a total of 16,103 clinical samples originating from veterinary facilities of five German federal states in 2007. Of all samples examined, 72 were positive for MRSP, giving an overall prevalence of 0.45%. In clinical specimens originating from small animals the prevalence was 0.58% ( n = 67; dogs n = 61 and cats n = 6), while samples from equidaes revealed a prevalence of 0.10% ( n = 5; horses n = 4, donkey n = 1). Forty-six representative phenotypically identified MRSP were further differentiated by DNA-based species assignment, PCR detection of mecA, SCC mec-typing and MIC determination. As expected, all 46 isolates were unambiguously proven to be MRSP by sequencing of housekeeping genes pta and cpn60 and being positive for mecA. Furthermore, all isolates harboured the mobile staphylococcal cassette chromosome mec (SCC mec) SCC mecIII. Antibiotic susceptibility testing for 20 different conventional antimicrobial agents disclosed a high rate of multidrug-resistant isolates (45 of 46) displaying an identical or at least similar resistance pattern for non-β-lactam antimicrobials. The recognized prevalence of MRSP, which have already been shown to be potential zoonotic agents, reflects the recently emerging development of these serious and often multidrug-resistant pathogens in Germany.