Owing to their high abundance in eukaryotic genomes, bisexual mode of inheritance and hyper‐mutability, microsatellites have quickly developed into an invaluable tool in molecular and wildlife genetics. Despite their widespread application, microsatellites have only marginally been used in studies utilising ancient/historical materials. This is primarily because of the characteristics inherent to such materials, that is, a low abundance of autosomal deoxyribonucleic acid (DNA) and a high degree of degradation resulting in endogenous DNA of insufficient length for microsatellite amplification. The few studies that have combined microsatellites and historical materials have helped to uncover information otherwise irretrievable from contemporary materials. The last decade's advances in sequencing technologies are both foe and friend to future investigations utilising microsatellites and historical materials. Although sequencing genomes of extinct specimens has never been easier and attract a lot of attention, such projects might inadvertently identify novel microsatellite loci, a powerful prospective tool for population‐wide assessments of past genetic variation.

Key Concepts:

• Owing to characteristics such as their omnipresence in eukaryotic genomes, high mutability, multiallele state and ease of typing, microsatellites have been a prominent marker in molecular ecology over the past 20 years.
  
• The peculiarities of DNA obtained from historical and ancient specimens hamper the successful application of microsatellites to such sample materials.
  
• Although not very numerous, studies that have combined microsatellites and historical materials have unravelled genetic variation otherwise lost in time.
  
• Recent advances in sequencing techniques are helping to quickly discover new microsatellite loci and will potentially enable the time‐ and cost‐effective generation of multilocus genotypes of the innumerable specimens hidden in natural history museums.