In arid areas, many herbaceous plants tend to be associated with woody plants.  Annual plant communities under shrub canopies are typically more species rich and distinct in structure and species composition from communities between shrubs.  Since arid areas are marked by inter-annual changes due to strong rainfall fluctuations, we investigate whether the structure and composition of annual communities differ between microhabitats.  We present plant community data from contrasting desert substrates from 1994 to 2007 in the Mojave Desert in order to explore these questions:  (1) Are communities under canopies more stable than communities in open areas?  (2) Are communities on sandy substrates more stable than communities on fine-textured soil?  (3) Do wet years promote non-native annuals over natives?  On sandy soil, species richness tends to be rather stable both under shrubs and in open.  This is in contrast to communities on fine textured soils where fluctuation in species richness was high both in the open and the subcanopy.  Species composition as measured with multivariate analysis underlies strong fluctuations for sandy soils under the canopy but not so in the open.  This is in contrast to fine-textured soils where subcanopies vary more than open areas.  Overall there are stronger fluctuations on fine-textured soils than on coarse sandy soils.  Surprisingly, the proportion of non-natives within the annual plant community actually increased in relative dry years.  This increase is reversed however during prolonged drought.  The study demonstrates that relative site quality is effecting community structure in a very complex and dynamic manner.