Abstract: 【Objective】 The present study aimed to study the genome-wide variation situation of Lihe super late-maturing aborted-seeded mutant GLL-1, and provide theoretical basis for regulating the ripening period of litchi fruit, analyzing Molecular mechanisms of aborted-seeds, and breeding of aborted-seeded litchi varieties.【Method】 Through the survey of litchi germplasm resources, Lihe super late-maturing aborted-seeded mutant GLL-1 was found, whole-genome resequencing of cultivars Heli and GLL-1 with 50×depth was conducted, and GLL-1 whole-genome variation situations were compared.【Result】 Compared with Heli, the GLL-1 fruit was obviously larger, with good quality, especially late ripening, seeds became into aborted-seeds, the edible rate was greatly improved. Obtained a total of 320858674 high quality clean reads from GLL-1 genome, of which 96.07% were located in the reference genome of litchi, and the percentage of bases with the correct recognition rate greater than Q20 was 96.48%. The percentage of bases with the correct recognition rate greater than Q30 was 91.38%;the genomic GC content was 35.28%, 97.62% of bases with a depth of more than 1×were covered. The results revealed 9306084 single nucleotide polymorphisms(SNPs) and 759887 insertion and deletion of small fragments(Indels), which conferred 12621 mutant genes. A total of 8451 non-synonymous SNP mutations and 4170 Indel genes were identified. It was worth noting that many anthocyanin biosynthesis associated transcription factor family genes including MYB, b HLH and WD40 and important family genes involving in ABA signal transduction including bZIP, WRKY, MAPK and PPR were mutated.【Conclusion】 Mutations in family genes, including MYB, bHLH, WD40, bZIP, WRKY, MAPK and PPR, may be a major cause of the super late ripening and the aborted-seeded traits of GLL-1 fruit, which play a key role in regulating litchi fruit development and aborted-seeded traits.