To develop synthetic varieties (Syn) of broccoli for organic agriculture, we initiated a breeding programme from a landrace (LR). A Syn was obtained through a farmer-assisted selection programme that mirrors the original LR. The diversity level of the Syn was assessed using 14 putatively neutral microsatellite markers (simple sequence repeats (SSR)) and seven SSR related to genes involved in flowering control. Four commercial F1 hybrids were also assessed. Despite the strict selection procedure applied by the farmer to reproduce the LR annually and to obtain the Syn, the detected diversity level was high and similar to that of non-selected LRs. The possible reasons for these genetic outcomes (i.e. SSR position in the genome and farmer selection methods) are discussed here.