The seeds of Arabidopsis thaliana become encapsulated by a layer of mucilage when imbibed. This polysaccharide-rich hydrogel is constituted of two layers, an outer layer that can be easily extracted with water and an inner layer that must be examined in situ in order to study its properties and structure or disintegrated through hydrolysis or physical means in order to analyze its constituents. Mucilage is an adaptive trait and a detailed analysis of both layers of mucilage has been carried out for 19 natural accessions showing atypical outer mucilage traits. The natural accessions were obtained from the Versailles Arabidopsis Stock Center (http://publiclines.inra.fr/naturalAccession/index) and are listed according to their Versailles identification number. Biochemical assays of mucilage extracts or in situ analyses using stains and antibodies or TD-NMR were used to generate a dataset of over 182 000 values covering 33 traits measured in four biological replicates.