The properties of globular cluster systems (GCSs) in the core of the nearby galaxy clusters Fornax and Hydra I are presented. In the Fornax cluster we have gathered the largest radial velocity sample of a GCS system so far, which enables us to identify photometric and kinematic sub-populations around the central galaxy NGC 1399. Moreover, ages, metallicities and [α/Fe] abundances of a sub-sample of 60 bright globular clusters (GCs) with high S/N spectroscopy show a multi-modal distribution in the correlation space of these three parameters, confirming heterogeneous stellar populations in the halo of NGC 1399. In the Hydra I cluster very blue GCs were identified. They are not uniformly distributed around the central galaxies. 3-color photometry including the U-band reveals that some of them are of intermediate age. Their location coincides with a group of dwarf galaxies under disruption. This is evidence of a structurally young stellar halo “still in formation”, which is also supported by kinematic measurements of the halo light that point to a kinematically disturbed system. The most massive GCs divide into generally more extended ultra-compact dwarf galaxies (UCDs) and genuine compact GCs. In both clusters, the spatial distribution and kinematics of UCDs are different from those of genuine GCs. Assuming that some UCDs represent nuclei of stripped galaxies, the properties of those UCDs can be used to trace the assembly of nucleated dwarf galaxies into the halos of central cluster galaxies. We show via semi-analytical approaches within a cosmological simulation that only the most massive UCDs in Fornax-like clusters can be explained by stripped nuclei, whereas the majority of lower mass UCDs belong to the star cluster family.