棘龙科包含两个亚科:重爪龙亚科、棘龙亚科。棘龙亚科是由塞里诺在1998年所命名,并由汤玛斯·荷兹(Thomas R. Holtz Jr.)等人在2004年定义为:亲缘关系较接近埃及棘龙,而离沃克氏重爪龙较远的所有物种。重爪龙亚科则是由查理格(Alan J. Charig)与Angela C. Milner在1986年所建立,它们为了新发现的重爪龙属建立了重爪龙科与重爪龙亚科;后来重爪龙被发现与棘龙科有关。汤玛斯·荷兹等人在2004年将重爪龙亚科定义为:亲缘关系较接近沃克氏重爪龙,而离埃及棘龙较远的所有物种。
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