The cryptic invasion of golden apple snails (Pomaceaspp.) in Taiwan has caused significant ecological and economical damage, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity and potential path of invasion ofPomaceaspp. across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations from 14 counties or cities across Taiwan. We identified and compared the genetic diversity ofP. canaliculataandP. maculatabased on mitochondrial COI in Taiwan, as well as other introduced and native countries (publicly available COI data) to understand the possible paths of invasion in Taiwan. Based on mitochondrial COI barcoding, sympatric but heterogeneous distributions of invasiveP. canaliculata(widespread) andP. maculata(mostly restricted to Southern Taiwan) were noted. Our haplotype analysis and mismatch distribution suggest multiple introductions ofP. canaliculatalikely originated directly from Argentina, whereasP. maculatawas probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil, instead of directly from Brazil. Our population genetic data further demonstrated higher haplotype and genetic diversity forP. canaliculataandP. maculatain Taiwan compared to other Asian countries, which also suggest multiple introductions affected Taiwan. Comparing the introduction history, current distribution and cryptic nature ofP. canaliculataandP. maculatain Taiwan, we posit thatP. maculatawas likely introduced along withP. canaliculata(either intentionally or unintentionally), whereas,P. canaliculataplausibly has several diverse introduction histories. Based on our current understanding, the establishment ofPomaceaspp., is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.