分子系統遺傳學和進化致力于使達爾文的夢想觸手可及——“擁有每個大自然王國相當真實的系譜樹。”該雜志為分子研究提供了一個論壇，促進我們對系統發育和進化的理解，進一步發展系統發育上更精確的分類，并最終為所有的分支生命線帶來統一的分類。如果系統地理學研究提供了特殊的理論或實證進展，將考慮出版。該雜志鼓勵多學科的文章，特別是在領域，如生物信息學，計算生物學，分子生物學和有機體生物學，是有興趣的社區的系統和進化生物學家。此外,報告新發現或見解的進化過程和機制上表達了在分子水平上是受歡迎的,就像那些處理重建從分子進化歷史數據的方法(如描述的新的或更強大的計算機算法從同源核苷酸或氨基酸序列構建系統發育樹)。對分子進化機制和過程的深入理解，將有助于建立更精確的分子進化模型，從而有助于開發更好的算法，從序列數據重建進化歷史。基于少數分類單元、單個分子標記或使用基于密碼子的方法測試達爾文選擇陽性的論文，但在缺乏實驗證據的情況下，即所謂的選擇氨基酸變化導致適應性表型效應，將不被接受。

Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.The journal encourages articles that are multidisciplinary, especially in areas, such as bioinformatics, computational biology, molecular biology, and organismic biology, that are of interest to the community of systematic and evolutionary biologists. In addition, presentations of new findings on or insights into evolutionary processes and mechanisms as expressed at the molecular level are welcome, as are those that deal with the methodology of reconstructing evolutionary history from molecular data (such as descriptions of new or more powerful computer algorithms for constructing phylogenetic trees from orthologous nucleotide or aminoacid sequences). A deeper understanding of the mechanisms and processes of molecular evolution should lead to more accurate models of molecular evolution, which in turn should facilitate the development of better algorithms for reconstructing evolutionary history from sequence data.Papers based on few taxa, single molecular markers, or that use codon-based methods to test for positive Darwinian selection, but in the absence of experimental evidence that allegedly selected amino acid changes cause an adaptive phenotypic effect, will not be accepted.