These data describe delivery of novel gene silencing agents (GSAs) to leaf tissue of the invasive common reed <i>Phragmites australis</i> ssp. <i>australis</i> using cell penetrating peptides (CPPs). These CPPs were tested for their ability to infiltrate <i>P. australis</i> leaf tissue using confocal microscopy. In addition, a series of novel gene silencing agents targeting a putative phytoene desaturase (<i>PDS</i>) gene were developed including twelve antisense oligonucleotides (ASOs), five artificial microRNAs (amiRNAs), and amiRNA-expressing plasmids and a cassette. GSAs were applied to living <i>P. australis</i> plants in conjunction with cell penetrating peptides and an infiltration medium at multiple charge ratios and application frequencies. Reduced expression of <i>PDS</i> was then characterized using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Confocal microscopy and qPCR results are available herein.