[Aim] Tuta absoluta is an important pest of tomatoes worldwide and seriously threatens the development of the tomato industry. Understanding its genetic diversity can reveal variations in the genetic structure of geographically different populations. [Method] Inter-simple sequence repeat (ISSR) molecular markers were used to analyze the genetic diversity and genetic structure characteristics of 20 geographical populations of T. absoluta. [Result] A total of 137 ISSR bands was amplified using 15 ISSR primers, among which 96.35% were polymorphic bands. All individuals showed unique ISSR patterns. Genetic diversity analysis of ISSR markers revealed that the genetic distance ranged from 0.0065 to 0.1623 in 20 geographical populations and genetic consistency ranged from 0.8502 to 0.9935. According to the analysis of the source of population variation, 25.36% of the genetic variation arose from among populations and 74.64% from within the population. In unweighted par group method with arithmetic mean phylogenetic analysis, the clustering of each geographic population had no strong correlation with geographic location. [Conclusion] Studies of T. absoluta invasion are still in early stages; however, and frequent invasions from different regions are commonly observed. Quarantine may be necessary to blockfurther invasion events from different regions.