Ramaria has been a remarkable taxon throughout the history of macrofungi. However, there is a lack of information on these macrofungi. This study determined the order of nucleotides in the mitochondrial genomes (mitogenomes) of three Ramaria species, followed by a detailed investigation of the obtained genetic information. Circular mitogenomes of Ramaria brunnecliacina, R. ichnusensis, and R. flavescens had sizes of 78,960, 61,851, and 81,282 bp, respectively. The genomes exhibited variations in genetic content, gene length, tRNA, and codon usage. Ramaria mitogenomes demonstrated variable evolutionary rates across several protein-coding genes. Results revealed significant gene rearrangements in Ramaria mitogenomes, including gene displacement and tRNA duplication. Bayesian inference and maximum likelihood methods, yielded well-supported phylogenetic trees for Basidiomycota. Phylogenetic analysis, using a comprehensive collection of conserved mitochondrial proteins, yielded a strong and reliable phylogenetic tree for Basidiomycetes, which clarified the evolutionary connections between Ramaria and other Basidiomycetes members. R. brunnecliacina and R. flavescens were identified as closely related species. Species of Ramaria, a paraphyletic group, exhibited a close genetic relationship with other species belonging to the subclass Phallomycetidae. This study presents a basic structure for understanding the evolutionary dynamics, genetic makeup, and taxonomy categorization of this significant fungal community.