This paper reports on a molecular dynamics investigation of the molecular organization of alkanethiolates (from ethane to dodecanethiolate) on octahedral and cubic gold nanocrystals with diameters up to 10 nm. We show that the average surface per adsorbed thiolate only slightly depends on the nanocrystal shape and the alkane chain length. Two different organizations of thiolates are observed on the facet centers and edges of octahedral nanocrystals, while on cubic nanocrystals only one appears. This explains the closer distance between thiolates on the edges of octahedral nanocrystals, which is not observed for nanocubes. The enhanced surface coverage of thiolates on nanocrystals is explained by the new organization for octahedral nanocrystals and can be attributed to the occupation of adsorption sites on the edges for cubic nanocrystals. Small differences observed in the molecular organizations on icosahedral and octahedral nanocrystals can be mainly explained by the larger facets of the latter ones.