Abstract: The brine shrimp Artemia inhabit hypersaline ecosystems of salt lakes and coastal saltworks around the world. Being a small zooplankton, Artemia serves not only an important part of the food chain and biological regulator in the brine ecosystem, but also a crucial live food item in marine fish and crustacean larviculture. This study aimed to investigate whether the population genetic diversity, genetic structure, and morphological characteristics of Artemia franciscana originated from San Francisco Bay saltpan have been changed during the coexistence with local parthenogenetic Artemia populations after artificial inoculation in the Bohai Bay saltworks. Five batches of Artemia cysts collected in previous years (1990—2021) included A. franciscana population from SFB, USA in 1990, A. franciscana population from Vinh Chau saltworks, Vietnam in 2018, parthenogenetic Artemia population from BHB Chengkou saltworks in 1990 (before inoculating A. franciscana), and two populations from BHB Tanggu saltworks in 2010 and BHB Chengkou saltworks in 2021 (after inoculating A. franciscana). The cysts were hatched separately and Artemia nauplii were reared till adult for morphometric measurement. Genomic DNA was extracted from each adult, followed by amplification and sequencing of the COI gene. The genetic diversity and genetic structure of different populations before and after inoculation were analyzed by using the COI gene sequences, and the genetic structure among different populations and their adaptive changes in new habitats were explored. The results showed that the inoculation and colonization of SFB A. franciscana in Bohai Bay saltworks has led to an increase in the genetic diversity of local Artemia population. A. franciscana has outcompeted the BHB indigenous parthenogenetic Artemia population as a dominant species, putting the native parthenogenetic population at risk of extinction. The fact that SFB population had no significantly genetically differentiation from the BHB Chengkou and Tanggu populations, confirming that these populations were directly introduced from the SFB population. Morphometric analyses revealed that introduction of the SFB Artemia into BHB saltworks resulted in decreasing cyst diameter and increasing male body length in the mixed BHB Artemia population. Similarly, the decrease of cyst diameter also occurred after the introduction of the A. franciscana into Vinh Chau, Vietnam. These results indicate that A. franciscana possesses strong environmental adaptability and morphometric plasticity, which supports its establishment and broader ecological amplitude during competitive coexistence. This study provides valuable insights into biodiversity in saltworks ecosystem and offers guidance for the conservation and management of Artemia germplasm resources.