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A field study was conducted to monitor the effect of different desert shrub ecophysiological adaptations on the composition, size, and diversity of soil free-living amebae. Population diversity was also analyzed using four morphological types. Samples were collected seasonally under the canopy of the common desert shrubs Artemisia herba alba, Reaumuria negevensis, and Noea mucronata. Control samples were taken from exposed interspace areas between shrubs. The composition and diversity of the ameba population were significantly affected by both season and plant species. Types 3 and 4 amebae were found to create a complementary system of adaptation in which type 3 was resistant and adapted to the harsh environment, whereas type 4 was much more vulnerable and existed for short periods of time when the environment allowed. The Reaumuria negevensis ecophysiological adaptation had a negative effect on type 4 amebae by creating a stressed environment.