Abstract Conyza sumatrensis and Conyza bonariensis are two important hexaploid weed species that impact crop production systems across the globe. Here, we report reference genome assemblies for both species. The sequenced accession of C. sumatrensis is resistant to multiple herbicides and was collected from the state of Paraná in Brazil, while the accession of C. bonariensis was collected from California, USA. Genomic long read data was used along with optical mapping data to assemble the C. sumatrensis genome into a single haplome at chromosome-level contiguity. The same approach was used along with chromatin contact mapping data to phase the haplotypes of C. bonariensis and generate two chromosome-level haplome assemblies. Subgenome-specific sequences were identified and used to classify the three subgenomes within each assembly. The assemblies are highly complete based on the presence of conserved single-copy orthologs and telomeres, and the size of these assemblies agrees with previous flow cytometry estimates. Full-length transcript sequencing along with gene models from other Asteraceae members was used to predict gene models within each assembly. The genomic resources reported here will be useful for investigations into evolutionary and ecological questions around weed invasion and management for these two species.