PMAT is an efficient toolkit for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. It addresses the challenges of frequent recombination and horizontal gene transfers in plant mitogenomes, which often lead to incomplete and inaccurate assemblies. PMAT has been applied to the assembly of 13 plant mitogenomes, outperforming existing organelle genome assemblers in terms of accuracy and completeness. The toolkit can achieve a complete plant mitogenome assembly with only 1× HiFi sequencing data, significantly reducing the need for mtDNA isolation and manual corrections. PMAT includes a Singularity container and scripts for recruiting target mitochondrial contigs from third-generation WGS data, generating reliable mitogenome assembly graphs. The study demonstrates the effectiveness of PMAT in assembling mitogenomes of various plant species, including eudicots, monocots, gymnosperms, and bryophytes, and provides valuable resources for plant evolution and phylogeny studies.PMAT is an efficient toolkit for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. It addresses the challenges of frequent recombination and horizontal gene transfers in plant mitogenomes, which often lead to incomplete and inaccurate assemblies. PMAT has been applied to the assembly of 13 plant mitogenomes, outperforming existing organelle genome assemblers in terms of accuracy and completeness. The toolkit can achieve a complete plant mitogenome assembly with only 1× HiFi sequencing data, significantly reducing the need for mtDNA isolation and manual corrections. PMAT includes a Singularity container and scripts for recruiting target mitochondrial contigs from third-generation WGS data, generating reliable mitogenome assembly graphs. The study demonstrates the effectiveness of PMAT in assembling mitogenomes of various plant species, including eudicots, monocots, gymnosperms, and bryophytes, and provides valuable resources for plant evolution and phylogeny studies.