| Summary: | In this work, using simple sequence repeat (SSR) markers, we present new insights into the genetic diversity, differentiation, and structure of <i>Beta vulgaris</i> subsp. <i>maritima</i> of western Iberia and the Azores and Madeira islands and of <i>B. macrocarpa</i> from southern Portugal. <i>B. macrocarpa</i> occurs only in southern Portugal and frequently in sympatry with <i>B. vulgaris</i> subsp. <i>maritima</i>, showing genetic introgression. <i>B. macrocarpa</i> has a better-defined structure than <i>B. vulgaris</i> subsp. <i>maritima</i>, which has a high degree of admixture. A great differentiation (F<sub>ST</sub> ranging from 0.277 to 0.184) was observed among the northern populations of <i>B. vulgaris</i> subsp. <i>maritima</i>. In contrast, only a small differentiation (F<sub>ST</sub> ranging from 0.000 to 0.026) was detected among the southern <i>B. vulgaris</i> subsp. <i>maritima</i> populations. The inland <i>B. vulgaris</i> subsp. <i>maritima</i> populations (“RIO” and “VMT”) are distinct from each other, which also occurs with the two islands’ populations (“MAD” and “AZO”). The existence of two distinct Atlantic Sea currents can explain the fact that Madeira is related to the southern populations, while the Azores is related to the northern populations. We consider that understanding the relationships existing within <i>Beta</i> spp. is key to future genetic studies and for the establishment of conservation measures. Our results show that the southern coastal areas of Portugal should be considered as a potential site for in situ conservation of the beet wild relatives. Special attention is needed in what concerns <i>B. macrocarpa</i> because this is a rare species that also occurs in a sympatric relationship with <i>B</i>. <i>vulgaris</i> subsp. <i>maritima</i>.
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