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Nurse-plants generally have positive effects on understorey species by creating more suitable conditions for stress-intolerant plants relative to open micro-habitats. However, long-term effects of this plant-plant facilitation system have been rarely examined. Seeds of five desert annual species from Atiquipa coastal desert in Southern Peru were used to examine whether different microenvironmental conditions under the nurse-plants Caesalpinia spinosa Molina (Kuntze) lead to differences in seed biology and germinability of annual plants relative to open, canopy-free conditions. Seeds collected from plants associated with nurse-plants were predicted to be (i) larger due to more favourable growing conditions, (ii) more viable and with greater germination rates, (iii) less variable in size and viability due to reduced environmental heterogeneity, and (iv) to germinate faster to avoid apparent competition with other annuals. Seed attribute measurements and germination trials in growth chambers were used to test these predictions. Although the plant abundance of only 2 of 5 species was strongly facilitated by the nurse-plant, no significant differences were found in seed mass, viability or relative variability between understorey and open micro-habitats for any of the species. Contrary to our predictions, final seed germination rates of seeds from open micro-habitats were higher, and the open micro-habitat treatment was more favourable for germination of seeds from both open and understorey environments. Taken together, these results suggest that plant-plant facilitation does not necessarily affect seed biology traits. Further studies addressing larger distribution ranges and/or density gradients of understorey species will illuminate the potential evolutionary effects of nurse-plants.