Researchers developing new cultivars of red raspberry (Rubus idaeus subsp. idaeus L.) and black raspberry (R. occidentalis L.) observe progeny of breeding populations for several seasons to identify those that perform reliably. If a portion of any breeding population could be eliminated based on a qualitative character or molecular marker, resources used for that portion could be used for other progeny. Our objective is to identify such molecular markers for red raspberry and black raspberry. A black raspberry × red raspberry cross was made to develop a map of each parent, and an F2 population was generated to join the maps. Simple sequence repeat (SSR) markers derived from red raspberry and strawberry were used. The level of homozygosity for the red raspberry was 40%, and the level for the black raspberry was 80%. Severe segregation skewing was observed in the F2 generation and indicates problems with transmission. Our findings help quantify the relative levels of homozygosity previously reported for red raspberry and black raspberry. In addition, the severe skewing observed in the F2 generation provides a molecular perspective to the fertility problems previously reported for the black raspberry × red raspberry hybrids (purple raspberry). Since black raspberry is highly homozygous, purple raspberry has transmission and fertility problems, and black raspberry breeders have reported a frustratingly low level of diversity in this subgroup, development of a black raspberry map is expected to require twice the markers as for a red raspberry map, emphasizing the need for a black raspberry sequence from which to develop molecular markers.