[3] The first published description of this species was made in June 2002 by John Atwood and Stig Dalström of Marie Selby Botanical Gardens, and Ricardo Fernandez from the San Marcos National University Herbarium (USM).

[2] An independent description prepared by orchid taxonomist Eric Christenson was published just afterwards in July 2002, using the name Phragmipedium peruvianum,[4] which thereby became a synonym of P. kovachii.

[6][5][7] Michael Kovach, an American orchid collector[8] who bought the live type specimen of P. kovachii from a roadside vendor in Peru, had smuggled the plant into the US and taken it to the Selby Botanical Gardens.

[11] While Selby Botanic Gardens saw its CITES permit revoked, was sentenced to a fine of $5000, and staff member Wesley Higgins received a 6-month restriction order.

[3] A nomenclatural proposal was put forward in 2006 to declare the name Phragmipedium kovachii invalid and to add its original ad hoc publication "Selbyana vol.

[14] Despite its inclusion in Appendix I of CITES, there's criticism on the measure, as it is believed that it is an ineffective tool against smuggling as it slows the introduction of wild species in the legal market.

[3][14] Due to the reduction of its population by overcollection and its small area of extent, Phillip Cribb (orchid expert from Kew Gardens) and the IUCN have assigned Phragmipedium kovachii the critically endangered conservation status.

[3][1] Phragmipedium kovachii will thrive in any moist growing medium with calcium content similar to the soil of its habitat, always watching for the pH levels.