In 1993, a population of freshwater glass shrimp (Paratya australiensis) was translocated from Kilcoy Creek to Branch Creek in the Conondale Range, Queensland. Subsequent genetic analysis revealed that the translocated and resident shrimp belonged to different mitochondrial DNA lineages (mtDNA) that were capable of hybridising. Monitoring of the pools along Branch Creek up until 2002 suggested that the translocated lineage had an advantage in upstream pools, and the resident lineage dominated downstream. Differential temperature tolerance and hybridisation barriers such as hybrid inviability and mate selection were factors proposed to explain hybrid zone structure. The major objective of this study was to combine nuclear and mtDNA markers to identify the structure of the hybrid zone in 2013 and identify any changes that had occurred since 2002. Specifically, we used genetic data to test for evidence of hybrid zone movement, and used FIS values to investigate whether mating was random in the contact zone; where hybridisation barriers could be present. The results revealed that the hybrid zone centre has shifted 510m downstream since 2002. Increased rainfall in the region since 2010 could have facilitated this. Secondly, mating appears significantly non-random in the pools where both lineages occur; supporting the occurrence of hybridisation barriers which appear to prevent the co-occurrence of the two lineages in the same pool. This study reveals a complex and dynamic hybrid zone, and exemplifies why multiple temporal studies are necessary to understand hybrid zone structure.