The collection was formed from individual donations only in the last quarter of the 19th century. The core of the entire collection is a set of 600 gemstones which was donated to the National Museum by the keen minerals collector, Doctor Vojtěch Wraný. Our largest olivine, found in Kozákov (inventory no. P1D168), with a square brilliant cut (16.7 × 16.7 mm), weighing 15.67 ct; the bright yellow orthoclase crystals from Madagascar with a rectangular step cut (P1D578; 26.5 × 22.7 mm; 50.43 ct) and an octagonal brilliant cut (P1D579, 10.01 × 9.6 mm, 2.55 ct); and the yellow-green chrysoberyl from Sri Lanka with a square brilliant cut (P1D72; 18.8 × 17.4 mm; 27.80 ct) – all come from this donation.

The grammar school professor Vilém Vařečka from Písek donated to the National Museum gemstones found in pegmatite in Písek, many of which are unique; for example, the golden beryls (no. P1D80) with cushion and oval brilliant cuts (17 × 14.5 mm; 18.55 ct). Thanks to Prof. Vrba's many connections with notable mineralogists and collectors from around the world, and thanks to many other donors (Alois Oliva, Karel Rummel and others), the collection quickly expanded. After Vrba’s death, the management of the collection was taken over by Ludmila Slavíková, who headed the department until 1939.

The collection expanded considerably after World War II due to property confiscations. Confiscations brought two yellow diamonds from Kimberley (P1D3512; 24.08 ct, and a smaller one of 11.95 ct), which are to this day the largest diamonds in the collection. In the 1950s and 1960s, the National Museum received a donation of several large collections; for example, from the State Heritage Institute in Prague (unique varieties of quartz – amethyst, rock crystal, smoky quartz, citrine, and also precious opal, aquamarine and a collection of synthetic gems). At this time, the collection was also enriched by a collection of unique amethysts, smoky quartzes and aquamarines from Murzinka in the Urals, turquoise minerals and also a star ruby.

In the 1970s and 1980s there were some purchases of high quality gemstones of rare size. Among these were a rich green beryl (P1D3531, rectangular step cut weighing 424.64 ct), a rich violet sapphire (P1D4184; 13.6 × 1 × 2.8 mm; 13.86 ct) with the combined Ceylon cut, with clearly-visible haloed rutile and zircon inclusions. This period, until 1991, was closely connected with RNDr. Jiří Kouřimský CSc. The scientific processing and popularization of this collection is largely to his credit.

In 1991 the collection came under the management of Mgr. Petra Burdová, who was behind the creation of the modern permanent exhibition in the safe-room style called the Cabinet of Precious Stones, which the public was able to admire until 2010. In this period, Svatopluk Prchlík was the most generous donor, enriching the collection with, for example, a citrine from Madagascar in a non-traditional multi-faceted cut in the shape of a dahlia (P1D4913; 37.4 × 37.92 mm; 197.47 ct). In 2016, exceptionally clear smoky quartz and rock crystal gemstones from the Vysočina region were bought from Vladislav Urban. A faultless, tall, smoky brown quartz with emerald cut (P1D4919; 73 × 67 mm; 1325 ct), can serve as a representative specimen from this purchase.
Since 2016 the sub-collection has been managed by Mgr. Lukáš Zahradníček F.G.G., whose aim is to perform a systematic inventory of it and to document it photographically. The inventory will include certification of the rarest and most precious pieces in the sub-collection. As of 6. 9. 2018, the collection contained 4,922 inventory numbers, which represent approximately 9,000 individual pieces, making it the largest collection of its kind in the Czech Republic, and one of the largest in Europe.