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The 2nd Moscow International Conference "Molecular Phylogenetics" (MolPhy-2) provided a stimulating platform for the exchange of ideas and experiences, cross-disciplinary interactions, and long-term national and international collaborations. Its major focus was to discuss the modern state of molecular phylogenetics and systematics, the interfaces between molecular and phenosystematics, molecular phylogenetics of different organisms, and the development of natural classification systems. The conference was dedicated to the memory of Professor Andrey Antonov, the founder of the Russian molecular phylogenetics school.