The site of Kozarnika in Bulgaria is a key, deep (~6 m) archaeological sequence spanning the Lower, Middle and Upper Palaeolithic of Europe. In its latter phases, it documents the transition from a Neanderthal-dominated Europe, to one in which only modern humans are present. The process of this transition is of major importance to understanding the timeline of hominin dispersals, extinctions and replacement in Europe. We obtained 37 new AMS radiocarbon dates to build a robust chrono-stratigraphy for the site through sampling humanly modified bones, artefacts and human remains. We focussed particularly on dating the Initial Upper Palaeolithic phase of the occupation, in geological layer 6/7, because of its potential link with early dispersing Homo sapiens populations. We built a series of Bayesian models of the results to test the inclusion or exclusion of various determinations. We used a KDE model approach to plot the entire set of results, and compared them with others regional sites. The KDE Models show that the latter phases of human occupation at Kozarnika comprised five distinct periods, dated between about 50-26,000 years ago. We found that the 6/7 phase ranged from 48,500-44,050 cal BP, probably starting from about 49,960 cal BP. We think the most likely occupants at this time are modern humans, as indirectly evidenced by a Homo sapiens tooth found within the same context. The stone tool evidence from the site contains some Levallois pieces, however, with echoes of the earlier Middle Palaeolithic. This mix of stone tools of different traditions may represent interstratification – with alternating visits by both Neanderthals and modern humans. Aside from the evidence from Apidima (Greece) which dates to about 210,000 years ago [1], Kozarnika is the earliest site found in eastern Europe from the last 100,000 years which contains evidence for the presence of modern humans. Neanderthal presence might in fact extend closer to 43,130-41,490 cal BP (95.4% prob.), ended by the start of the earliest Kozarnikian industry at the cave; the Kozarnikien très ancien, as elsewhere in Europe with similar industries. The application of sediment DNA approaches might help to unlock further evidence about the humans that were present during this crucial period, as the Middle Palaeolithic ended and the early Upper Palaeolithic began.