Taq polymerase system is one of the key success factors for genotyping by using semi-random marker types. Start codon targeted (SCoT) and sequence-related amplified polymorphism (SRAP) are semi-random markers that amplify more than one target at a time, like in multiplex PCR. Here, we compared the performance of five multiplex PCR kits (QIAGEN®, Thermo Scientific™, New England Biolabs, KAPA Biosystem and iNtRON Biotechnology) and Taq DNA polymerase from Vivantis as a representative common Taq polymerase. The PCR using three SCoT and three SRAP markers was performed in six plants, which were different in genome size, including three monocotyledons (rice, oil palm and onion) and three dicotyledons (holy basil, chilli pepper and eggplant). The overall results demonstrated consistent high performance of the Taq polymerase system with the multiplex PCR kit from KAPA Biosystem. Considered by plant, the multiplex PCR kit from KAPA Biosystem showed the best performance in holy basil, eggplant, oil palm and chilli pepper, whereas in rice, the Taq DNA polymerase from Vivantis generated better results than the KAPA Biosystem. In onion, multiplex PCR kit from Thermo Scientific™ showed the best performance among those tested, even if it did not perform well in the other plans. Different Taq polymerase systems might generate different band patterns, therefore using the same Taq polymerase system within one experimental dataset is recommended. The multiplex PCR kit from KAPA Biosystem is the best starting choice.