The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein—the predatory mite family Phytoseiidae—molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within‐genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.

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The objective of this study was to carry out a large survey in order to characterize Phytoseiidae species diversity on cassava in Kenya. A total of 29 species from 10 genera were identified in diverse ecological zones in Kenya. The warm-to-hot low midlands of eastern and the warm-humid coastal strip yielded over 70 % of the species identified. The dominant species were Euseius fustis (Pritchard and Baker) and Typhlodromalus aripo De Leon present in 37 and 34 % of samples, respectively. Typhlodromalus aripo was found persistent in coastal, eastern and western regions of Kenya while E. fustis was present in all sampled localities of the country. In addition to morphological diagnosis, molecular sequences for DNA fragments 12S, CytB, COI and ITS, were obtained for T. aripo and E. fustis. Molecular diagnosis has revealed the unexpected presence of Neoseiulus idaeus Denmark and Muma and indicated its misidentification as Neoseiulus onzoi (Zannou, Moraes and Oliveira) in a previous survey carried out in Kenya. Molecular sequences herein obtained will help further diagnosis of phytoseiid species and complement the international reference databases needed to assist molecular identification of Phytoseiidae species.