This protocol describes a method for screening transgenic lines of Phaeodactylum, specifically for those obtained via conjugation with episomal plasmids. The assay can also be used for screening genomic integrants obtained through biolistics. The assay uses patched colonies of diatom grown on agar plates for biomass and does not require the use of kits or any pre-processing (boiling, etc) of the samples prior to analysis. This allows for relatively high-throughput screening of transgenic lines in a single day.