A putative staphylococcal protein A (spa) gene was discovered in the genome of Staphylococcus pseudintermedius and used for developing a species-specific spa typing protocol. Thirty-one clinical methicillin-resistant S. pseudintermedius (MRSP) isolates from dogs and cats in four countries were characterized by spa typing, pulsed-field gel electrophoresis (PFGE) and staphylococcal cassette chromosome (SCCmec) typing. The results indicated the occurrence of two MRSP clones that acquired distinct SCCmec elements in Europe (t02, PFGE type A, SCCmec type III,) and California (t06, PFGE type B, SCCmec type V). Sequence analysis of mecA revealed the occurrence of four alleles (mecA1 to mecA4), which correlated with the geographical origin of the isolates and enabled discrimination of two distinct subtypes within the European clone. The newly developed spa typing method appeared to be a promising tool for easy and rapid typing of MRSP, either alone or in combination with SCCmec and mecA typing for fine-structure epidemiological analysis.