Despite the beneficial nutritional value of strawberries, there is a potential risk of allergic reactions in consuming strawberries, especially for people with Bet v 1 allergy. Allergen content varies in the fruits depending on environmental and genetic backgrounds, also involving the fruit color. Diploid strawberry varieties on the European market, bearing white and red colored fruits (‘Blanc Amelioré’, ‘Weiße Hagmann’, ‘Weiße Solemacher’, ‘Yellow Wonder’, ‘Rote Baron Solemacher’, ‘Walderdbeere’) in addition to a new accession VM2012 were characterized by microsatellite analyses. Three strawberry varieties with white colored fruits, ‘Weiße Hagmann’, ‘Weiße Solemacher’, ‘Yellow Wonder’, were very similar to each other, but ‘Blanc Amelioré’ and VM2012 could be distinguished from the other varieties. The allergen genes fra a 1 and fra a 3 of diploid red and white colored strawberry varieties and VM2012 were identical on genomic level. Of the eight gene variants described for fra a 1 in octoploid strawberries (Fragaria × ananassa) only the gene variant fra a 1 A2 was highly conserved present in the diploid varieties of Fragaria vesca, indicating a role of F. vesca in the phylogeny of octoploid strawberries. For fra a 3, the sequence differed only in a single nucleotide exchange T503C from the octoploid sequence of the variety ‘Camarosa’, with no effect on the protein sequence. No complementation with regard to the fruit color was observed in crosses between VM2012 and the white colored diploid varieties ‘Weiße Hagmann’ and ‘Weiße Solemacher’ indicating that the genetic cause behind the white fruit color might be similar.