Camelina microcarpa is one of the closest relatives of Camelina sativa, an important oilseed crop belonging to Brassicaceae. The availability of diploid, tetraploid and hexaploid species of Camelina are instrumental to infer the evolutionary trajectory of Camelina and elucidate the fate of duplicated genes in the neopolyploid Camelina species. Here we generated three new genome assemblies of C. microcarpa; one tetraploid CN119243 (2n = 26), and two hexaploids with divergent chromosome numbers, Type 1 - CN119205 (2n=40) and Type 2 - CN120025 (2n=38). The tetraploid genome (CN119243) and Type 1 hexaploid genome (CN119205) were sequenced using Oxford Nanopore Technology and Pacific BioScience Technology, while the Type 2 hexaploid genome (CN120025) was sequenced using Pacific BioScience Technology. A novel sub-genome structure was identified in the C. microcarpa Type 2 genome. Hi-C analysis indicated that the proximity of homoeologous chromosomes may play a role in gene expression bias in polyploid species. Comprehensive gene and repeat annotation, as well as syntenic relationship among Camelina species, are further described in the following manuscript.