Cauliflower production is hindered by variation in curd quality and maturity. Morphological variation from seed to harvest is due to genetic variation interacting with environmental conditions and here the genetic factors were investigated. The aim of this study was to search for DNA markers linked to seedling traits, facilitating early selection of seedlings in cauliflower production. Cauliflower seed lines were germinated in Petri dishes (20°C, 7 days) and seedlings were transferred to pots and grown under glasshouse conditions. Seed weight and various seedling characters were measured until harvest at 6 weeks. DNA was extracted using the CTAB method and RAPD markers were identified using 17 primers. Multivariate analysis based on principal coordinates analysis was used to correlate morphological traits with molecular markers across cultivars. Markers associated with seed weight, germination rate, shoot length, root length, fresh weight, and dry weight were identified.