Marker assisted selection (MAS) permits the selection of plants carrying genes that control interesting agronomic traits through the screening of associated markers; this allows the breeders to retain only germplasm conferring desirable traits from an early stage. Usually MAS involves the screening of hundreds or thousands of seedlings and thus the main challenge faced is the development of a pipeline that starts with a “lab friendly” and unambiguous seedling disposition in greenhouse, allows the rapid collection of samples avoiding cross contamination, implements a fast, cost-effective, high-throughput method of DNA extraction to be used for a small number of PCRs, and utilizes robust, reliable, and easy to interpret molecular markers. In this study ~6,500 seedlings from 24 apple crosses were genotyped in order to select seedlings conferring resistance traits, fruit quality traits or both. Lab work was performed using the KAPA 3G Plant PCR kit. The main problems encountered were associated with dirty extractions; however, following optimization less than 10% of the seedlings had to be resampled and in total about 70% of the samples tested carried desirable traits.