Abstract The weed flora of the reclaimed desert lands in the eastern and western stretches of Qena Governorate along the Nile Valley was investigated. This study attempted to identify the vegetation groups (communities) prevailing in common winter and summer crops, to recognise the crop–weed relationships, and to assess the role of different soil factors on the distribution and composition of the weed flora in each season. Three major crops were selected: alfa–alfa (winter and summer seasons), wheat (winter season) and millet (summer season). Altogether, 146 studied fields (stands) were monitored, and distributed as follows: 49 in the wheat fields, 38 in alfa– alfa (summer season), 24 in alfa–alfa (winter season), and 35 in millet fields. Frequency (f %) of weed species within the different crop farmlands was used as measure of ecological success. The total number of species varied among the studied crops: the highest was 131 species in alfa–alfa (the perennial crop), followed by 111 species in wheat (the winter crop), and the lowest (29 species) was in millet (the summer crop). The relationships between the recorded species and crops were discussed. TWINSPAN as a classification method and DCA as an ordination methods were used to assess differences in floristic composition in different seasons. The resulted TWINSPAN vegetation groups from winter and summer seasons were clearly separated along the first 2 axes of DCA. Canonical correspondence analysis was used to evaluate the relationships between the examined soil factors and the floristic presence/absence data sets in each season.