A method for the detection and analysis of mitochondrial genomic DNA material, mitochondrial RNA material and proteic material in a eukaryotic cell and for the detection of the occurrence of initiation of replication events in mitochondrial genomic DNA in a eukaryotic cell, comprising the steps of: - contacting said eukaryotic cell comprising said mitochondrial genomic DNA with a first nucleotide probe under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the mitochondrial DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said mitochondrial DNA genome, wherein the first nucleotide probe is specific for a segment of non transcribed mitochondrial gDNA and comprises or consists of: i. the nucleic acid of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, or fragments thereof, or, ii. a nucleic acid that has at least 80% identity with the nucleic acid sequence of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, said nucleotide probe being a single strand molecule ranging in size from 90 to 150bp, in particular from 95 to 110bp, preferably sizing 99 bp, and, - contacting said eukaryotic cell with at least a second nucleotide probe targeting at least one mitochondrial RNA molecule corresponding to a transcribed region of a mitochondrial DNA molecule in the cell, wherein the second nucleotide probe comprises or consists of: iii. the nucleic acid of SEQ ID N°17 or SEQ ID N°18, or a fragment thereof, or iv. a nucleic acid that has at least 80% identity with the sequence SEQ ID N°17 or SEQ ID N°18, said second nucleotide probe being a single strand molecule ranging in size from 100 bp to 2000 bp, and, - contacting said eukaryotic cell with a probe targeting at least one protein of interest within said eukaryotic cell, and - detecting said first nucleotide probe hybridized to said mitochondrial DNA and said second nucleotide probe hybridized to said mitochondrial RNA molecule, and - detecting the probe hybridized to said protein of interest, in particular by immunofluorescence. - contacting said eukaryotic cell comprising said mitochondrial genomic DNA with a first nucleotide probe under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the mitochondrial DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said mitochondrial DNA genome, wherein the first nucleotide probe is specific for a segment of non transcribed mitochondrial gDNA and comprises or consists of: i. the nucleic acid of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, or fragments thereof, or, ii. a nucleic acid that has at least 80% identity with the nucleic acid sequence of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, said nucleotide probe being a single strand molecule ranging in size from 90 to 150bp, in particular from 95 to 110bp, preferably sizing 99 bp, and, i. the nucleic acid of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, or fragments thereof, or, ii. a nucleic acid that has at least 80% identity with the nucleic acid sequence of any one of SEQ ID N°1 to SEQ ID N°16 or a complement thereof, - contacting said eukaryotic cell with at least a second nucleotide probe targeting at least one mitochondrial RNA molecule corresponding to a transcribed region of a mitochondrial DNA molecule in the cell, wherein the second nucleotide probe comprises or consists of: iii. the nucleic acid of SEQ ID N°17 or SEQ ID N°18, or a fragment thereof, or iv. a nucleic acid that has at least 80% identity with the sequence SEQ ID N°17 or SEQ ID N°18, said second nucleotide probe being a single strand molecule ranging in size from 100 bp to 2000 bp, and, iii. the nucleic acid of SEQ ID N°17 or SEQ ID N°18, or a fragment thereof, or iv. a nucleic acid that has at least 80% identity with the sequence SEQ ID N°17 or SEQ ID N°18, - contacting said eukaryotic cell with a probe targeting at least one protein of interest within said eukaryotic cell, and - detecting said first nucleotide probe hybridized to said mitochondrial DNA and said second nucleotide probe hybridized to said mitochondrial RNA molecule, and - detecting the probe hybridized to said protein of interest, in particular by immunofluorescence.