During the last twenty years, Cydia pomonolla granulovirus (CpGV, Baculoviridae) has become the most important biological control agent for the codling moth (CM). All registered products in Europe are based on the isolate CpGV-M. A threat to future CpGV application is the occurrence of resistant CM field populations. Since 2003, populations with up to 10,000-fold resistance were reported. An alternative are novel CpGV isolates which overcome CM resistance. This thesis focuses on the identification of resistance overcoming isolates and their molecular differences to CpGV-M. Isolates of different geographic origins were tested in bioassays. Five isolates were able to completely overcome CM resistance. Their genomes were compared by restriction fragment length polymorphism (RFLP) analysis. For unequivocal identification of CpGV isolates, a method based on single nucleotide polymorphisms (SNPs) was established. Whole genome sequencing of three genomes was performed. Comparison on open reading frame (ORF) level revealed only one protein alteration in resistance overcoming isolates compared to CpGV-M.