Biological invasions pose substantial threats to global biodiversity, agriculture, and ecological stability. Among these, intraspecific cryptic invasions, characterized by the spread of nonnative genotypes within a species, present unique challenges for detection and management. Despite the well-documented influence of invasive ants on ecosystems, instances of intraspecific cryptic ant invasions have rarely been documented. This study focused on the black cocoa ant, Dolichoderus thoracicus (Smith 1860), which has been increasingly reported as a pest inTaiwan over the past decade. In this study, we utilized a genome-wide approach employing multiplexed inter-simple sequence repeats genotyping by sequencing to identify single nucleotide polymorphisms across the D. thoracicus populations, elucidating the variations in the genetic population structure of the species in Taiwan. Our findings confirmed the occurrence of intraspecific cryptic invasions, demonstrating the coexistence of native and nonnative lineages, along with potential hybridization events between them. This study underscores the critical role of comprehensive genetic analysis in uncovering the complex dynamics of species invasions.