Clonally propagated crops have high levels of heterozygosity both between subgenomes within a somatic cell and between cells within an individual clone. Recent developments in 2^nd and 3^rd generation sequencing technologies have enabled the identification of this diversity, making it increasingly clear that these sources of diversity are abundant in clonal varieties and can contribute to variation in traits of interest to breeders. Compared with citrus cultivars like Sweet Orange, there are relatively few described accessions for Mexican lime (Citrus x aurantifolia). Given that many of the described varieties of sweet orange have been derived from somatic variants, we were interested in examining this variation in Mexican lime to assess its potential for further development of this cultivar. Using a recently published diploid assembly of Mexican lime and high-coverage PacBio HiFi libraries from leaf tissue of four individuals, we identified multiple large structural variants differing between thorned and thornless lineages, and evidence for mosaicism at hundreds of loci. Many of these variants are found in the promoters and bodies of genes and may act as standing variation for continued improvement of this cultivar.