House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Past studies of wild-caught mice across latitudinal and temperature gradients provided evidence of environmental adaptation in traits related to body size, body proportions, and metabolism. Moreover, genome-wide scans identified candidate genes underlying adaptive differences. However, the contribution of transposable elements (TEs) to environmental adaptation remains unknown in wild populations of house mice. Here, we used PacBio long-read whole-genome sequencing toinvestigate the genomic distribution and variation of TEs, including their classification, distribution, and abundance in wild populations inhabiting contrasting temperate and tropical environments (New Hampshire-Vermont, USA, and Manaus, Brazil). We sequenced 20 individuals to a minimum 25-fold coverage, generating genome assemblies for each individual (N50=20-54 Mb). We identified and classified TEs using RepeatModeler and MCHelper. We manually curated TE library call-sets for both populations, improving TE identification and resolving unknow classifications. Across both wild populations, LINE/L1 and LTR/ERVsuperfamilies were the most frequently identified TEs. Moreover, we observed that TEs occupy approximately 30% of the genome, with LINE 1 being the most abundant (~14% of the genome). Additionally, we identified over 92,000 structural variants (SVs) across all 20 genomes. Compared to mouse inbred strains and human populations, we find 1.8x and 4.5x more SVs, respectively. Our future directions will involve investigating the contribution of structural variation and TE polymorphism to environmental adaptation in natural populations of house mice.