In this study, three possibly smuggled marble statues of an unknown origin, two human torsi (a female and a male) and a small head, were subjected to molecular analyses. The aim was to reconstruct the history of the storage of each single statue, to infer the possible relationship among them, and to elucidate their geographical shift. A genetic strategy, comprising metagenomic analyses of the 16S ribosomal DNA (rDNA) of prokaryotes, 18S rDNA of eukaryotes, as well as internal transcribed spacer regions of fungi, was performed by using the Ion Torrent sequencing platform. Results suggest a possible common history of storage of the two human torsi; their eukaryotic microbiomes showed similarities comprising many soil-inhabiting organisms, which may indicate storage or burial in land of agricultural soil. For the male torso, it was possible to infer the geographical origin, due to the presence of DNA traces of Taiwania, a tree found only in Asia. The small head displayed differences concerning the eukaryotic community, compared with the other two samples, but showed intriguing similarities with the female torso concerning the bacterial community. Both displayed many halotolerant and halophilic bacteria, which may indicate a longer stay in arid and semi-arid surroundings as well as marine environments. The microbiomes retrieved from each statue showed to be very specific, but some individual members showed to be biological markers for the geographical regions through which the pieces traveled and for the conditions under which they were stored.