Independent isomeric yield ratios (IYR) of 81Ge, 96Y, 97Y, 97Nb, 128Sn and 130Sn have been determined in the 25 MeV proton-induced fission of natU and 232Th. The measurements were performed at the Ion Guide Isotope Separator On-Line (IGISOL) facility at the University of Jyväskylä. A direct ion counting measurement of the isomeric fission yield ratios was accomplished for the first time, registering the fission products in less than a second after their production. In addition, the IYRs of natU were measured by means of γ-spectroscopy in order to verify the consistency of the recently upgraded experimental setup. From the obtained results, indications of a dependence of the production rate on the fissioning system can be noticed. These data were compared with data available in the literature, whenever possible. Using the TALYS code and the experimentally obtained IYRs, we also deduced the average angular momentum of the fission fragments after scission.