We report the first experimental determination of independent isomeric yield ratios using direct ion counting with a Penning trap, which offered such a high resolution in mass that isomeric states could be separated. The measurements were performed at the Ion Guide Isotope Separator On-Line (IGISOL) facility at the University of Jyväskylä. The isomer production ratios of 81Ge, 96,97Y, 128,130Sn, and 129Sb in the 25-MeV proton-induced fission of natU and 232Th were studied. Three isomeric pairs (81Ge, 96Y, and 129Sb) were measured for the first time for the natU(p,f) reaction, while all the reported yield ratios for the 232Th(p,f) reaction were determined for the first time. The comparison of the experimentally determined isomeric yield ratios with data available in the literature shows a reasonable agreement, except for the case of 130Sn for unspecified reasons. The obtained results were also compared with the gef model, where good agreement can be noticed in most cases for both reactions. Serious discrepancies can only be observed for the cases of 96,97Y for both reactions. Moreover, based on the isomeric yield ratios, the root-mean-square angular momenta (Jrms) of the fission fragments after scission were estimated using the talys code. The experimentally determined isomeric yield ratios, and consequently the deduced Jrms, for 130Sn are significantly lower compared to 128Sn for both fissioning systems. This can be attributed to the more spherical shape of the fragments that contribute to the formation of 130Sn, due to their proximity to the N=82 shell closure. The values of Jrms for 129Sb are higher than 128Sn for both reactions, despite the same neutron number of both nuclides (N=78), indicating the odd-Z effect where fission fragments with odd-Z number tend to bear larger angular momentum than even-Z fragments. The isomer production ratio for the isotopes of Sn is more enhanced in the natU(p,f) reaction than in 232Th(p,f). The opposite is observed for 96Y and 97Y. These discrepancies might be associated to different scission shapes of the fragments for the two fission reactions, indicating the impact that the different fission modes can have on the isomeric yield ratios.