We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age (‘Late Minoan’) period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to determine the local baseline values. We then measured the strontium and sulphur values of humans from Late Neolithic and Bronze Age sites. Our results indicate that most of the humans have sulphur and strontium isotope values consistent with being local to Crete, showing no evidence for a wide-scale movement of people from the Greek mainland or other areas away from Crete in these time periods. However, we found four individuals from the late Bronze Age (Late Minoan III) cemetery of Armenoi with sulphur isotope values not typically found in Crete and are instead consistent with an origin elsewhere. This cemetery at Armenoi also has one of only a few examples of the newly adopted Mycenaean Linear B script on Crete found outside of the palace sites, pointing to an influence (trade and possible migration) from the mainland, which may then be the place of origin of these four individuals. DNA (mtDNA) studies of eight Late Bronze Age individuals from Armenoi have results consistent with people living in Aegean region at this time and cannot be used to distinguish between individuals from Crete (‘Minoans’) and the Greek mainland [‘Mycenaeans’]).