Citrus tristeza virus (CTV) is the most economically important pathogen of citrus in the north of Iran. CTV exists as a number of distinct strains with different biological properties. Seven isolates of CTV were collected from the north of Iran and all induced stem pitting and vein clearing on Mexican lime (Citrus aurantifolia), but caused widely differing symptoms on sour orange (Citrus aurantium), Duncan grapefruit (Citrus paradisi) and Thomson naval orange (Citrus sinensis) grafted onto sour orange. Based on symptoms in different host plants, the isolates could be divided into two groups: the first causing stem pitting and severe decline and the second, seedling yellows. Isolates in the first, but not the second, group were transmitted by Aphis gossypii. The major coat protein (CP) gene was amplified by immunocapture reverse transcriptase polymerase chain reaction to yield an amplicon of 672 bp for all isolates. Analysis of the nucleotide and the deduced amino acid sequences of the CP genes showed minimal genetic variation. Interestingly, in a phylogenetic analysis, the isolates from the eastern part of Mazandaran Province grouped apart from previously characterised isolates from the western part of Mazandaran Province, suggesting at least two independent introductions of the virus into Iran. The nucleotide sequence of the CP of the Iranian isolates were 96–98%, 96–97% and 97–98% identical to the Japanese NUagA, Korean Chenju and Californian SY568 isolates, respectively. No clear association was found between CP gene sequence, symptomatology and transmissibility by A. gossypii.