Phenotyping is a modern technology that allows registering and analyzing data about living systems phenotypes in automatic mode. In recent years a high-efficiency higher plants phenotyping with the aim of deep study of the physiological and biochemical bases of their functioning, as well as selection of new high-yielding and stress-resistant varieties has acquired significant development. It is based on adaptation and introduction of modern information approaches such as algorithms of «computer vision» and allows receiving detailed information about plants phenomes at various organization levels. One of the unreached research sections in this field is tree plant cuttings phenotyping, which represents a great practical interest. In this work the system of phenotyping of green stem cuttings of woody plants Thuja occidentalis L. (Smaragd), Juniperus scopulorum Sarg. (Blue Arrow), Picea Abies L., H. Karst. was developed using machine vision algorithms and spectral analysis. A modular phenomics complex was created. It consist of phenomics box, plant cultivation system, lighting and watering systems, as well as system of registration and processing of RGB-images, including software. This complex has been tested in the laboratory and in field conditions. The initial testing of the phenomics complex was carried out. It showed that the data of changes in the pixel distribution of RGB-images by wavelengths can be the basis for estimating the size and physiological state of stem cuttings of woody plants. It was shown that the shift of the spectral curve of the reflected light into the long-wave area under the influence of water deficit allows to non-invasive and statistically reliably register the death of some cells. At the same time, statistically reliable distinctions have not been revealed at testing of influence of phytohormones (auxins and brassinosteroids) on rooting of stem cuttings of coniferous species. The obtained results have a fundamental practical significance and can be used in the research of physiological processes in higher plants, ornamental crop production and forestry.