:Due to extensive introduction and breeding, the classification relationship of Lonicera L. is unclear. We need scientific methods to explore the classification of these new Lonicera. In this paper, the pollen morphology characteristics, karyotype features, floral and fruit pigment components of 13 taxa of Lonicera were analyzed by means of scanning electron microscopy, karyotype analysis, HPLC-MS and GC-MS. 13 taxa of Lonicera were respectively divided into four, three, three and three groups through the analysis of pollen morphology characteristics, karyotype features, floral and fruit pigment compositions. Lonicera ruprechtiana and Lonicera tatarica can always be clustered together. Five hybrids such as Lonicera korolkow × Loniceramaackii., Lonicera korolkow × Loniceratatarica No.8 et a can basically clustered with their parents. These results indicate that the analysis of pollen morphology characteristics, karyotype features, floral and fruit pigment composition has value and significance for the study of system classification and systematic relationship, and the conclusions of this study partially support morphological taxonomy.