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A microwave assisted method was used to synthesize RhAu nanoparticles (NPs). Characterization, based upon transmission electron microscopy (TEM), energy dispersive spectroscopy, and powder X-ray diffraction, provided the evidence of monomodal alloy NPs with a mean size distribution between 3 and 5 nm, depending upon the composition. Extended X-ray adsorption fine-structure spectroscopy (EXAFS) also showed evidence of alloying, but the coordination numbers of Rh and Au indicated significant segregation between the metals. More problematic were the low coordination numbers for Rh; values of ca. 9 indicate NPs smaller than 2 nm, significantly smaller than those observed with TEM. Additionally, no single-particle structural models were able to reproduce the experimental EXAFS data. Resolution of this discrepancy was achieved with high resolution aberration corrected scanning TEM imaging which showed the presence of ultra-small (<2 nm) pure Rh clusters and larger (∼3–5 nm) segregated particles with Au-rich cores and Rh-decorated shells. A heterogeneous model with a mixture of ultrasmall pure Rh clusters and larger segregated Rh/Au NPs was able to explain the experimental measurements of the NPs over the range of compositions measured. The combination of density functional theory, EXAFS, and TEM allowed us to quantify the heterogeneity in the RhAu NPs. It was only through this combination of theoretical and experimental techniques that resulted in a bimodal distribution of particle sizes that was able to explain all of the experimental characterization data.