分子生態學發表論文，利用分子遺傳學技術來解決生態學、進化、行為和保護方面的重要問題。研究可使用中性標記推斷生態和進化過程，或檢查生態上重要的基因及其產物。我們還在我們的伙伴期刊《分子生態資源》上發表關于技術方法、計算機程序和基因組資源開發的文章。然而，主要是描述性的和只與正在研究的分類單元相關的論文應該提交給更專業的期刊。分子生態學的研究領域包括:生態、進化和種群基因組學人口結構與系統地理學環境基因組學群落生態學與共同進化生殖策略親緣關系和親緣選擇性分配人口的遺傳理論分析方法開發保護遺傳學物種形成和雜交微生物生物多樣性qtl的演化動力學生態相互作用分子適應與環境基因組學轉基因生物的影響

Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products. We also publish articles on technical methods, computer programs and genomic resource development in our companion journal, Molecular Ecology Resources. However, papers that are primarily descriptive and relevant only to the taxon being studied should be submitted to a more specialized journal. Research areas of interest to Molecular Ecology include:ecological, evolutionary, and population genomics population structure and phylogeographylandscape genomicscommunity ecology and coevolutionreproductive strategiesrelatedness and kin selectionsex allocationpopulation genetic theoryanalytical methods developmentconservation geneticsspeciation and hybridizationmicrobial biodiversityevolutionary dynamics of QTLsecological interactionsmolecular adaptation and environmental genomicsimpact of genetically modified organisms