Neandertal permanent mandibular molars are well represented at Hortus Cave, France, Sub-Phase IVb and Vb, providing an opportunity to assess intrapopulation and intersite shape variation. We expected the mandibular molars from Hortus cave, comprising Hortus II, Hortus IV, Hortus V and Hortus VI to cluster together, compared to Neandertals close in proximity, such as Malarnaud and La Quina 5 as well as those more distantly located such as Arcysur- Cure 1, Engis 2 and Scladina 4A-1. A single Neolithic cave burial from Maurenne Caverne de la Cave, Belgium (n = 11) is used to contextualize the degree of variation in the Hortus assemblage. From photographic images of the permanent molars, crown shapes were digitized and binarized. The resulting images were processed in R using elliptical Fourier analysis and the resulting amplitudes of the harmonics were subjected to principal components analysis and hierarchical clustering. Hortus II and Hortus V, both from Sub-Phase Vb, are relatively similar to one another in M1 crown shape, and are secondarily grouped with Hortus IV from Sub-Phase IVb. Maurenne Caverne de la Cave has a larger degree of variation in crown shape than the Hortus assemblage, and the Neandertals imperfectly cluster together and apart from the Neolithic sample for some multivariate comparisons. Variance in Neandertal molar crown shape can be primarily explained as the result of chronology. Hortus consistently groups with other MIS 3 Neandertals such as La Quina 5 and Engis 2, while those from MIS 5, represented by Scladina 4A-1 and Malarnaud are distinct as is Arcy-sur-Cure 1 from late MIS 3. Across the molars, the Hortus assemblage is most similar to La Quina 5 from Charente, Southwest France.