This protocol describes (1) how to amplify the genomic markers SCAR3, SCAR4, SCAR5 and SCAR7 (developed by Thornhill et al., 2013) from genomic DNA of Aiptasia, (2) how to use Gibson Assembly® to clone them into a (pCR™II-TOPO®-derived) plasmid and (3) performing colony PCRs to screen for clones to sequence by Sanger sequencing. The subcloning is highly recommended since strains might be heterozygous for some or all of the markers. SCAR: Aiptasia-specific inter-simple sequence repeat (ISSR)-derived sequence characterized amplified region markers.Legal disclaimer:GIBSON ASSEMBLY® is a registered trademark of Synthetic Genomics, Inc.pCR™ and TOPO® are trademarks of Thermo Fisher Scientific and its subsidiaries.GoTaq® is a registered trademark of Promega Corporation.