In multiplex sequencing, DNA fragments from different samples are pooled and sequenced all together. The main reason is to increase sample throughput. The result is a mixture of sequencing reads from different samples. In a follow-up demultiplexing step, the reads needs to be separated by using the attached barcode (sample marker) sequences. This demultiplexing step usually is already done by your sequencing core facility.
https://www.illumina.com/science/technology/next-generation-sequencing/multiplex-sequencing.html