What are some limitations of the linnaean classification system?

In his Imperium Naturae, Linnaeus established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum. This approach, the Animal, Vegetable and Mineral Kingdoms, survives today in the popular mind, notably in the form of the parlour game question: "Is it animal, vegetable or mineral?". The work of Linnaeus had a huge impact on science; it was indispensable as a foundation for biological nomenclature, now regulated by the nomenclature codes.

But the system is based solely on physical characteristics, due to not having the proper technology to investigate the molecular data of animals