多核變形蟲缺乏線粒體和一些真核細胞的其他細胞器(如過氧化物酶體和高爾基體)。同時,由於沒有鞭毛,多核變形蟲也無法進行有絲分裂。多核變形蟲作為有核細胞卻缺乏其他真核生物所擁有的細胞器[11],一時間多核變形蟲被認為是真核生物原始的樣子,它們處於細菌和真核生物之間的過渡。[12]1973年,有人提出在沼澤多核變形蟲的祖先在其進化演變之前,真核生物已經開始出現線粒體。[13]在1976年,Jean M. Whatley寫道沼澤多核變形蟲可能是目前最原始的真核生物。[14]因此,多核變形蟲可能是現代真核生物的雛形。而根據共生體學說,共生的內部細菌,可能在後來演變為現代真核細胞的線粒體。這些共生細菌的功能目前仍不清楚,Whatley認為它們可能會提供一個進化的範例,來說明細菌到線粒體這種轉變方式。[14]
在1988年,多核變形蟲的原始形態又再一次被懷疑,Joe I. Griffin的研究表明沼澤多核變形蟲確實擁有不成熟的基礎鞭毛,它可以進行簡單的有絲分裂,Griffin表明多核變形蟲既不是真核細胞生物的原始形態,也沒有和其他變形蟲類存在很大的不同,它僅僅是一種變形體鞭毛蟲。[16]1995年,反對多核變形蟲屬於原始形態的呼聲越來越高,分子分析表明沼澤多核變形蟲的祖先很可能擁有線粒體。[17]幾年過後,很明顯,所有變形蟲綱的生物都被確認它們的線粒體已經消失。換句話說,多核變形蟲並不是處於早期的原始真核生物,而是已經退化並失去了它們祖先的細胞器的原生生物。[18]
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