The Bilbao Crystallographic Server came to life in 1997 as a scientific project by the [https://web.archive.org/web/20120127074622/http://lcdx00.wm.lc.ehu.es/lama/ Departments of Condensed Matter Physics and Applied Physics II] of the University of the Basque Country (EHU) under the supervision of J. Manuel Perez-Mato (EHU) and Mois I. Aroyo (EHU), in coordination with Gotzon Madariaga (EHU) and Hans Wondratschek (Karlsruhe Institute of Technology, Germany) with funding from the Basque government and several ministries of the Spanish government. The initial code was written by then Ph.D. students Eli Kroumova (EHU) and Svet Ivantchev (EHU) and the very first shells related to retrieval tools, group-subgroup relations and space group representations have soon appeared online.
Afterwards, in collaboration with Harold T. Stokes and Dorian M. Hatch from  Brigham Young University, USA, the server extended its services to include symmetry modes analysis. Asen K. Kirov, a Ph.D. student from Sofia University, Bulgaria contributed to the server, working on programs dedicated to irreducible representations and extinction rules.
In 2001, Ph.D. student Cesar Capillas began his research on the server and became the main developer and system administrator focusing on structure relations, such as pseudosymmetry and phase transitions. Danel Orobengoa, also a Ph.D. student, joined the developer team in 2005 and worked mainly on symmetry modes, k-vector classification tables and non-characteristic orbits (in collaboration with Massimo Nespolo of the Nancy-Université, France), writing his Ph.D. thesis on the applications of the server for ferroic materials.
In 2009, Ph.D. student Gemma de la Flor and post-doc Emre S. Tasci were recruited for the development team: de la Flor working mainly on the identification and interpretation of symmetry operations, structure comparison and Tasci becoming the new system administrator and main developer, focusing in the structure relations concerning phase transitions. The Bilbao Crystallographic Server team took its current (2012) line-up in 2010 with the addition of Ph.D. student Samuel Vidal Gallego, his main research field being the magnetic space groups.