A critical foundation of sustainable agriculture is to understand different agro-ecosystems components and to investigate relations between different species and environmental factors affecting their presence and expansion. The flora of Siwa Oasis agro-ecosystems was investigated and assessed. A total of 132 stands (66 in spring and another 66 in summer) were chosen to represent the study area and its soil properties during spring and summer. Cover of each species and foliage projective cover of each stand was visually estimated. Species richness, diversity and evenness were calculated for each stand. Soil analyses showed that stands could be differentiated geographically. Vegetation and soil relationships were explored using different ecological multivariate techniques. TWINSPAN classification resulted in four ecological groups in spring and four more groups in summer. DCA and DCCA clustered stands in a similar manner to the ecological groups extracted from TWINSPAN classification. Indicator species and correlated soil characteristics of each group were identified. Salinity, crop type, water availability, shade and human intervention are the major factors affecting the diversity and richness of the vegetation communities in Siwa Oasis cultivated land. Some of the species recorded are of high economic importance, highlighting a valuable opportunity to cultivate problematic soils with non-traditional crops.