Effector proteins secreted by fungi can alter plant functions, which then promotes parasitic growth. Sequence identification and functional annotation of secreted effectors are essential steps to understand the biology and molecular basis of host-pathogen interactions. Like other biotrophic fungi, Puccinia species possess large repertoires of secreted proteins, the vast majority of which have unknown functions or no sequence annotations. Using sequence clustering, we investigated the functional diversity of secreted effector protein families of P. kuehnii, the causal agent of sugarcane orange rust. We performed a large-scale family analysis with the predicted secretomes of isolates 1040 and 2143 of P. kuehnii and the secretomes of five other Pucciniales species (P. coronata, P. graminis, P. sorghi, P. striiformis, and P. triticina) using TribeMCL software. A total of 2,236 protein clusters were identified of which 436 were specific to P. kuehnii. Our long-term goal is to provide insights into the evolution of secreted protein families from rust fungal genomes.