The present invention relates to mutant strains of Mycoplasma hyopneumoniae and to a method for preparing said strains. It also relates to vectors used in said method, to vaccine compositions and to vaccine kits which comprise said strains for use against porcine enzootic pneumonia and other porcine diseases. The invention also relates to the use of M. hyopneumoniae as a host for the expression of recombinant proteins and other DNA sequences of interest.