在1881年,业余化石搜集者David Baldwin发现腔骨龙的第一个化石。在1889年,爱德华·德林克·科普(Edward Drinker Cope)将其命名为腔骨龙,当时他在与奥塞内尔·查利斯·马什(Othniel Charles Marsh)展开名为骨头大战的长期竞争[15]。模式种是鲍氏腔骨龙(C. bauri)是为向科普提供化石的乔治·鲍尔(George Baur)而命名。不过这套化石的保存状况很差,很难拼凑出腔骨龙的完整外貌。
于1947年,在美国新墨西哥州首次发现地点附近的幽灵牧场,发现了一个大量的腔骨龙尸骨层。这么多腔骨龙的化石可能是由突然的洪水所造成,将牠们集体冲走、掩埋。事实上,这类洪水在地球历史的这段时期甚为普遍,而亚利桑那州的石化林国家公园就是由一次类似的洪水所造成的。在1989年,埃德温·科尔伯特(Edwin H. Colbert)替所有已发现的化石进行了一次完整的研究[10],埃德温·尔伯特的研究提供很多有关腔骨龙的资料。幽灵牧场的大量标本,包括完整保存的标本,其中一个取代了原有的标本,而成为了作为分析的模式标本。
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