Microplastic contamination of marine environments is a global issue that affects wildlife health. There is scant information on microplastic load in marine megafauna, including piscivorous carnivores which likely accumulate microplastics from prey. This project examined microplastic loads in the Endangered endemic Australian sea lion (ASL, Neophoca cinerea), as part of a broader health study. We developed and validated a taxon-specific method for microplastic identification and isolation from ASL faeces, then utilised this new method to identify and count microplastics in scats sampled from three different regions, and across two colonies in Western Australia: Perth and Jurien Bay, and more remote Recherche Archipelago. Stable isotope analysis (δ15N and δ13C) was conducted on scats to investigate trophic/spatial variation in foraging behaviour between regions. Putative microplastics were found in 93% of sampled ASL scats and abundance ranged from 0–3.75 MP/g scat, with FTIR analysis currently underway. There were no differences in incidence nor abundance of microplastics within or amongst regions, despite obvious regional variation in foraging strategies by ASLs. ASLs in regions remote from human habitation appear to be as susceptible to microplastic contamination as those foraging near urbanised coasts. Dedicated studies investigating impacts of microplastics on health of ASLs are warranted.