Method for identifying the sample origin of adapter ligated and/or amplified sample DNAs comprising the steps of: a) providing a first and a second nucleotide sequence identifier, wherein each nucleotide sequence identifier is a nucleotide sequence of at least one nucleotide; b) providing adapters and/or amplification primers, wherein at least a first adapter or amplification primer comprises the first nucleotide sequence identifier and a second adapter or amplification primer comprises the second nucleotide sequence identifier, and wherein optionally, further adapter or amplification primers are provided comprising a further nucleotide sequence identifier; c) providing a plurality of sample DNAs; d) performing ligation and/or amplification reactions on the sample DNAs using the adapters and/or amplification primers, to provide adapter ligated and/or amplified prepared template DNAs for high throughput sequencing, wherein a prepared single-stranded template DNA comprises, in addition to a sequence captured and/or amplified from the sample DNA, a unique combination of the first and the second nucleotide sequence identifier and a first and a second sequencing primer binding site, and wherein the first sequencing primer binding site is located 3' of the first nucleotide sequence identifier and the second sequencing primer binding site is located 3' of the second nucleotide sequence identifier; e) determining at least the sequence of the first and the second nucleotide sequence identifier, wherein the first nucleotide sequence identifier sequence is determined in a first high throughput sequencing reaction using a first sequencing primer hybridizing to the first sequencing primer binding site and the second nucleotide sequence identifier sequence is determined in a second high throughput sequencing reaction using a second sequencing primer hybridizing to the second sequencing primer binding site and f) determining, based on the unique combination of the first and the second nucleotide sequence identifiers, the sample origin of the adapter ligated and/or amplified sample DNAs. a) providing a first and a second nucleotide sequence identifier, wherein each nucleotide sequence identifier is a nucleotide sequence of at least one nucleotide; b) providing adapters and/or amplification primers, wherein at least a first adapter or amplification primer comprises the first nucleotide sequence identifier and a second adapter or amplification primer comprises the second nucleotide sequence identifier, and wherein optionally, further adapter or amplification primers are provided comprising a further nucleotide sequence identifier; c) providing a plurality of sample DNAs; d) performing ligation and/or amplification reactions on the sample DNAs using the adapters and/or amplification primers, to provide adapter ligated and/or amplified prepared template DNAs for high throughput sequencing, wherein a prepared single-stranded template DNA comprises, in addition to a sequence captured and/or amplified from the sample DNA, a unique combination of the first and the second nucleotide sequence identifier and a first and a second sequencing primer binding site, and wherein the first sequencing primer binding site is located 3' of the first nucleotide sequence identifier and the second sequencing primer binding site is located 3' of the second nucleotide sequence identifier; e) determining at least the sequence of the first and the second nucleotide sequence identifier, wherein the first nucleotide sequence identifier sequence is determined in a first high throughput sequencing reaction using a first sequencing primer hybridizing to the first sequencing primer binding site and the second nucleotide sequence identifier sequence is determined in a second high throughput sequencing reaction using a second sequencing primer hybridizing to the second sequencing primer binding site and f) determining, based on the unique combination of the first and the second nucleotide sequence identifiers, the sample origin of the adapter ligated and/or amplified sample DNAs.