Background: Mitochondrial rRNAs contain site-specific modifications, including methylated residues, but few of the enzymes responsible for these modifications have been found. Results: RNMTL1, MRM1, and MRM2 are methyltransferase family members found associated with the mtDNA nucleoid and with the large ribosomal subunit. Conclusion:The association of putative RNA-modifying enzymes with nucleoids and ribosomes supports the model that assembly of mitochondrial ribosomes begins while rRNA transcription continues. Significance: This work advances understanding of the assembly of mitochondrial ribosomes necessary for biosynthesis of the respiratory chain.