Aims: Positive plant interactions can promote higher species density of beneficiary species in deserts. However, there is limited evidence examining the trait sets of seeds from beneficiary species. In this study, we examined the hypothesis that shrubs (benefactors) influence the germination of desert annuals (beneficiaries) and promote ecotypic differentiation by generating distinct microhabitats through abiotic stress amelioration. The following predictions were tested using growth chambers and field-collected seeds: (i) seed mass and viability will be greater and less variable for seeds collected from within shrub understory relative to seeds from open microhabitats, (ii) germination of seeds from shrub and open microhabitats will be greatest under simulated home (source) conditions, (iii) seeds from the shrub microhabitat will adaptively accelerate their germination rate when germinated in simulated home (source) microhabitats relative to their simulated away (reciprocal) microhabitat. Methods: Seeds and their associated maternal plants were collected from four annual species found within a shrub understory (Larrea tridentata) and open microhabitats in the Mojave Desert of California (35.30°N, 117.26°W, 793 m. a.s.l.), and then reciprocally germinated in growth chambers simulating both microclimatic conditions. Cumulative germination and germination rate was measured every 4-5 days for 42 days. Important Findings: There was no significant difference in the mean or coefficient of variation for seed mass and viability between the shrub and open microhabitats. The source of the seeds did not significantly impact the cumulative germination, and there was no accelerated rate of germination within potential species ecotypes thereby suggesting no ecotypic differentiation. Cumulative germination was significantly higher within the shrub-simulated microhabitat for three out of the four species examined. Cumulative germination and germination rate were significantly different between species. Hence, shrubs influence the germination of desert annuals, and the outcome of this interaction is species specific, but shrub microhabitats do not necessarily alter the more conserved seed biology traits. Future studies should examine the influence of gene flow on beneficiary adaptation and the influence of species-specificity on beneficiary species response to facilitation.