馬門溪龍最早是在1952年於四川的公路修築工地上發現。這個部份骨骸後來經研究,在1954年由著名的中國古生物學家楊鍾健命名為建設馬門溪龍(Mamenchisaurus constructus)。屬名意為「馬門溪的蜥蜴」,由漢語拼音mǎ「馬」+mén「門」+chi(xi的改寫)「溪」組成,意指化石最初發現地,位於四川宜賓金沙江的馬鳴溪渡口旁的建設工地,但由於楊的口音而將馬鳴溪龍誤作為馬門溪龍;[13]種名建設(constructus)則指第一具化石是在建築工地出土。[2]正模標本(編號IVPP AS V.790)來自上沙溪廟組的漢通組層位,年代為侏羅紀晚期牛津階。包含了14節不完整的頸椎。另外一個也是缺乏頭顱的部分骨骼(編號IVPP V948)也被歸入此種。[2]
在此之後,有其他多個物種陸續被命名。第二個有效種合川馬門溪龍(Mamenchisaurus hochuanensis),牠的模式標本編號為GCC V 20401,包含一個沒有頭骨的部分骨骼,保存了接近完整的19節頸椎。與模式種來自同一地層。最早於二戰之前在合川太平地區被發現,直到1957年四月才被挖掘出來,並於1965年在北京清修完成,由楊鍾健、趙喜進於1972年正式發表敘述。[3]文革期間,當時楊也擔心著自己的安全,於是這個標本的複製模型被大量製作出來,並送往中國以外以便保護;這些模型後來成為象徵著卡爾·馬克思推崇的演化理論的印證。複製品的問題在於頸椎沒有彼此分別開來,為了將其頸部彎曲,許多椎體中間被打斷並出現原本不存在的關節位置。2001年標本編號ZDM 0126被歸至合川馬門溪龍,包含頭骨、胸帶及前肢,都是正模標本缺失的部份。[14]總共有至少五具以上的標本被歸入此種。
葛瑞格利·保羅(英語:Gregory S. Paul)於2010年針對一些重要發現作了估計:他估計模式種建設馬門溪龍長15公尺及重5噸,並認為此種的頸部並未極度加長;而合川馬門溪龍的情況肯定不同,估計長20公尺及重14噸[10];1972年楊曾估計重達45噸。2016年的一份質量估計,根據21世紀北京製作的第二件骨架,由IVPP V456-V458三件標本組合而成,得出結論為最小估計值12063公斤。根據保羅於1988年的估計頸部長9.3公尺,在當時創下紀錄,[16]直到超龍(頸長14公尺)及波塞東龍(頸長11.5至12公尺)發表才被超越。[17]相對於身體長度,頸部非常細長,且尾部也較短,使頸長相當於其餘身體長度。後者觀點也適用於楊氏種,保羅估計長17公尺及重7噸;而他估計井研種長20公尺及重12噸。保羅同意博物館的模型並將其標示為中加種新標本的正確呈現,使其體長35公尺及重75噸,創下已發現的陸生骨骼的最大紀錄;[10]其頸部長17公尺,超越波塞東龍、梁龍的地震種、超龍的數值成為新紀錄;較小的模式標本頸長12公尺,頸肋長4.1公尺,也創下已敘述的最長蜥腳類頸肋記錄,長於波塞東龍的3.42公尺。[18]保羅亦認為安岳種大型,長25公尺及重25噸,同樣有極長頸部。[10][19]
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