Understanding of fertilization procedures and crossing barriers is essential for various plant breeding methods. Growth or inhibition of pollen tubes, therefore, is a crucial issue in terms of propagation, in particular concerning the determination of self incompatible (SI-) plants. In German Chamomile, vegetatively propagated SI-plants would be a highly appreciated breeding tool for the formation of maternal lines for specific crossings. Following the idea to enhance knowledge of aspects of pollination and to develop a fast procedure of determination of SI-plants, two different methods of microscopic analysis of pollen tube growth in pistils were developed. Under light and under fluorescence microscopy diverse stages of pollen tube growth could be made visible. These included growth starts at the stigma, active pollen tubes with regular callose deposits on their way through the style and globular stage embryos in the ovary. Furthermore, SI-tests and selections within six accessions of German Chamomile and among 220 plants were carried out. In this case, self incompatibility (SI) was determined as staying seedless after multiple hand pollination under crispac bag isolation, observed at not less than three flower heads per plant. Diploid varieties showed a tendency to establish SI, rather than their tetraploid relatives, although a high variability between accessions was given. An overall accordance between SI, examined via seed set, and evidence of pollen tubes could not be assessed. Nevertheless, new and detailed insight in fertilization procedures in German chamomile could be gained.