PMAT is an efficient toolkit for assembling plant mitochondrial genomes (mitogenomes) using low-coverage HiFi sequencing data. It enables the de novo assembly of 13 plant mitogenomes with high accuracy and completeness, outperforming existing organelle genome assemblers. PMAT requires only 1× HiFi sequencing data to assemble complete mitogenomes, making it cost-effective and efficient. The toolkit includes a Singularity container and scripts for assembling mitochondrial contigs from third-generation WGS data and generating reliable mitogenome assembly graphs. PMAT can be used for both plant mitogenomes and chloroplast genomes. It successfully assembled mitogenomes of 13 plant species, including eudicots, monocots, and gymnosperms, and evaluated the minimal sequencing data required for complete mitogenome assembly. The study demonstrated that PMAT can generate accurate mitogenome assembly graphs, allowing for the identification of multiple possible conformations. PMAT is efficient and cost-effective for assembling mitogenomes with large nuclear genomes and can be widely applied to plant mitogenome studies. The toolkit provides important genomic resources for plant evolution and phylogeny. PMAT is a valuable tool for plant mitogenome assembly, offering a more comprehensive and accurate approach compared to existing methods.PMAT is an efficient toolkit for assembling plant mitochondrial genomes (mitogenomes) using low-coverage HiFi sequencing data. It enables the de novo assembly of 13 plant mitogenomes with high accuracy and completeness, outperforming existing organelle genome assemblers. PMAT requires only 1× HiFi sequencing data to assemble complete mitogenomes, making it cost-effective and efficient. The toolkit includes a Singularity container and scripts for assembling mitochondrial contigs from third-generation WGS data and generating reliable mitogenome assembly graphs. PMAT can be used for both plant mitogenomes and chloroplast genomes. It successfully assembled mitogenomes of 13 plant species, including eudicots, monocots, and gymnosperms, and evaluated the minimal sequencing data required for complete mitogenome assembly. The study demonstrated that PMAT can generate accurate mitogenome assembly graphs, allowing for the identification of multiple possible conformations. PMAT is efficient and cost-effective for assembling mitogenomes with large nuclear genomes and can be widely applied to plant mitogenome studies. The toolkit provides important genomic resources for plant evolution and phylogeny. PMAT is a valuable tool for plant mitogenome assembly, offering a more comprehensive and accurate approach compared to existing methods.