Population genetic studies of lichen-forming fungi and their algae require appropriate sampling schemes that ensure representative sampling of the genetic variability. One question is whether mycobiont and photobiont populations require different sampling strategies. Here, I applied rarefaction methods to a dataset containing three microsatellite loci of Lobaria pulmonaria and three microsatellite loci of its green-algal photobiont, Dictyochloropsis reticulata. I analysed the sample sizes required for 1) the number of individuals per population, 2) the number of individuals required across a landscape and 3) the number of populations. The analyses were performed separately for the mycobiont and photobiont loci to detect any differences in the accumulation of genetic diversity among the symbionts that would require different sampling schemes. About 20 individuals were sufficient at the population level; within landscapes, 300–400 samples and about 25–30 populations covered most of the allelic diversity. The results indicated that a slightly higher sampling effort was required for the photobiont than for the mycobiont. The optimal sampling strategy strongly depends on the research question, the spatial scale of investigation, and the type of analysis to be performed with the data.