Poncirus trifoliata (L.) Raf. and trifoliate orange hybrid species comprise 90% of the citrus rootstock used in New Zealand. The resistance expressed by P. trifoliata to Citrus tristeza virus is in part responsible for the New Zealand citrus industry not suffering severe losses to this disease. However, isolates of Citrus tristeza virus have been identified in New Zealand that can overcome this resistance and establish a systemic infection of P. trifoliata. This study examined the coat protein (CP) and minor coat protein (CP_m) genes of endemic resistance-breaking (RB) and non-RB isolates at the molecular level. Both the major and minor coat genes of RB isolates were paraphyletic, with average nucleotide sequence identities of 95.2% and 92.1%, respectively. The RB isolates were phylogenetically distinct from non-RB isolates in both genes, with nucleotide identities ranging from 91.8 to 98.2% for the CP and from 91.0 to 96.9% for the CP_m. However, no correlation was found between specific nucleotide or amino acid polymorphisms in the CP or CP_m genes of these isolates and expression of the RB phenotype. These data suggest that the RB isolates comprise at least one or more distinct genotypes, distinct from known non-RB isolates.