Citrus tristeza virus (CTV) is endemic throughout the citrus production areas of South Africa and mild-strain cross-protection is employed to combat the negative effects of severe-strain infections. The country is among the world’s leading producers of grapefruit, however cross-protected trees often display severe stem grooving, regardless of the rootstock. Previously, cross-protection sources were evaluated empirically, through graft inoculations onto indicator hosts. Recent research has shown that cross-protection, possibly mediated by super-infection exclusion, is strain-specific. This, coupled with the varying affinities that cultivars display for different CTV strains, has shown the need to determine which CTV strains are associated with specific commercial cultivars. In this study, thirty-six Citrus paradisi (Macfad.) cv. “Marsh” plants were sampled in the South African grapefruit production areas of Malelane and Pongola. CTV populations from these samples were analysed through the amplification of the p33 gene and subsequent direct Sanger sequencing. A subset of 12 of these amplicons was selected for deep Illumina MiSeq sequencing. The resulting data showed high intra- and inter- orchard diversity of CTV, with populations showing similar genotype compositions to those found in recent studies on the “Star Ruby” cultivar. Populations were composed of a clearly dominant component, in most cases RB or Kpg3/SP/T3-like sequences, with at least two minor sequence types. AT-1-like and VT-like sequences were found to be dominant in only four and one of the analysed populations respectively. HA16–5, Taiwan-Pum/M/T5, T30 and B165 were present as intermittent minor components (less than 10% of mapped reads) across the populations.