Downy mildew disease of quinoa caused by Peronospora variabilis is a serious threat which greatly reduces yield. The identification of the source of the primary infection at the early growth stages of quinoa is necessary to manage the spread of this pathogen. Hence, a conventional detection method based on polymerase chain reaction (PCR) was applied to detect the DNA of P. variabilis in the tissues of the different organs of quinoa plants (radicle or root; cotyledon or leaf; hypocotyl or stem) at the different growth stages (5-, 10-, 15- and 21-days old plants) and in inflorescences (flowers and their axes) at 60 and 80 days old. Twelve composite quinoa seedling samples were subdivided into different organs at the different growth stages. P. variabilis was detected in cotyledon/leaf tissues (10/12; 83%), hypocotyl/stem tissues (41.6%; 5/12) and radicle/root was the least positive (1/12; 0.8%) for presence of the pathogen. Moreover, the PCR showed that the pathogen was detected in the flowers and in their axes at the ages of 60 and 80 days. The internal transcribed spacer (ITS) and cytochrome c oxidase subunit 2 (COX2) regions were examined. Phylogenetic analyses confirmed that P. variabilis (EGDM1) was the causal agent of downy mildew affecting quinoa in Egypt and genetically similar to the United States and China lineage (COX2 Maximum likelihood tree). Downy mildew pathogen was detected in different organs of quinoa plant at early growth stages and inflorescences. Hence, the pathogen can spread systemically in quinoa tissues.