The black truffle (Tuber melanosporum) is a heterothallic ascomycete. To investigate its sexual lifecycle, an experiment was settled up in situ to trace the genetic contribution of added crushed truffle fruitbody material (inoculum) on the produced fruitbodies in the following years. The dataset comprise the SSR genotyping data of T. melanosporum samples (gleba and spores separately), the associated metadata (sample information), and a table with information on the SSR.