<p><i>Ex situ</i> collections in botanic gardens safeguard plant species and their genetic diversity. While past research has typically used microsatellite markers to quantify the extent of <i>ex situ</i> genetic representation in botanic gardens, next-generation sequencing approaches generating thousands of single nucleotide polymorphisms (SNPs) have become more common. Several studies have examined the impact marker choice has on measures of genetic diversity and differentiation, but no evaluation on <i>ex situ</i> conservation metrics has been made. Additionally, minimum sample size estimates (MSSEs) for representing proportions of genetic diversity are typically reported as averages, but no study has quantified the variance surrounding MSSEs. To close these gaps, we simulated microsatellite and SNP data for species with various demographic characteristics and examined the impact different markers have on MSSEs and their variance. We found that using SNPs resulted in MSSEs twice as large as estimates based on microsatellites, and differences between SNP-based and microsatellite-based MSSEs were greater when total population sizes were larger. We also found that confidence intervals surrounding MSSEs are large, but can be decreased by using higher numbers of loci. Our results indicate that <i>ex situ</i> conservation metrics are sensitive to the marker type used, the number of markers, and the total size of wild populations, and that caution is needed when interpreting MSSEs based on empirical datasets that are small relative to a species’ total population size. We emphasize that the standard of conserving 95% of genetic diversity <i>ex situ</i> should be revisited, and that future minimum sample size recommendations to practitioners should incorporate uncertainty and account for the genetic marker being used.</p>