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Multiple particle tracking microrheology (MPT) is a powerful tool for quantitatively characterizing rheological properties of soft matter. Traditionally, MPT uses a single particle size to characterize rheological properties. But in complex systems, MPT measurements with a single size particle can characterize distinct properties that are linked to the materials' length scale dependent structure. By varying the size of probes, MPT can measure the properties associated with different length scales within a material. We develop a technique to simultaneously track a bi-disperse population of probe particles. 0.5 and 2 μm particles are embedded in the same sample and these particle populations are tracked separately using a brightness-based squared radius of gyration, R g 2 . Bi-disperse MPT is validated by measuring the viscosity of glycerol samples at varying concentrations. Bi-disperse MPT measurements agree well with literature values. This technique then characterizes a homogeneous poly(ethylene glycol)-acrylate:poly(ethylene glycol)-dithiol gelation. The critical relaxation exponent and critical gelation time are consistent and agree with previous measurements using a single particle. Finally, degradation of a heterogeneous hydrogenated castor oil colloidal gel is characterized. The two particle sizes measure a different value of the critical relaxation exponent, indicating that they are probing different structures. Analysis of material heterogeneity shows measured heterogeneity is dependent on probe size indicating that each particle is measuring rheological evolution of a length scale dependent structure. Overall, bi-disperse MPT increases the amount of information gained in a single measurement, enabling more complete characterization of complex systems that range from consumer care products to biological materials.