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Fennel (<i>Foeniculum vulgare</i>) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites&#8212;also known as simple sequence repeats (SSRs)&#8212;are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in <i>Daucus carota</i> for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.