The dataset comprises values of individual measurements of the two traits seed width and mucilage and seed width for 19 accessions having atypical outer mucilage properties (Fabrissin et al., 2019). Accessions are from the Versailles Arabidopsis stock center (http://publiclines.inra.fr/naturalAccession/index) and are listed by their Versailles identification number in a four-digit format. Seed lots were produced from plants in two cultivations series c or d and each lot is a bulk of seed from 10 - 12 individual plants. Measurements were obtained following immunolabelling and staining of seeds with an anti-RG-I antibody (INRA-RU1) and the cellulose specific fluorescent dye Direct Red 23 (DR23). As outer mucilage is lost during the immunolabelling procedure seeds analysed correspond to sample type 5 (inner mucilage and seed (hydrated). Observations was performed with a Zeiss LSM710 confocal microscope using 488nm or 561nm lasers to excite Alexa Fluor 488® or DR23, respectively. Fluorescence emission was detected between 500 and 550nm for Alexa fluor 488® and 565 and 640nm for DR23. For each seed lot, measurements were obtained from 30 seeds using Zen software. The dataset comprises 4560 values corresponding to measurements of 30 seeds from a seed lot.