Puccinia kuehnii, the causal agent of orange rust, is a fungal pathogen that causes damaging losses to the sugarcane crop in Florida since 2007. During plant infection, rust fungi deliver effector proteins into host tissues using a specialized feeding structure called a haustorium, to manipulate plant functions and promote parasitic growth. Identification of these effectors is therefore an essential step to understand host-pathogen interactions and to develop new control methods. In this study, two isolates of P. kuehnii from Florida were used for genome sequencing and effector discovery based on sequence features. Genomic DNA was extracted from spores of P. kuehnii 1040 and P. kuehnii 2143 that were collected from sugarcane cultivars CL 85-1040 and CP 89-2143, respectively. Short Illumina DNAseq and long read Pacbio sequencing was performed and a hybrid assembly was obtained for the genome of each isolate of P. kuehnii. These assemblies will be used as genomic resources for gene calling and proteome prediction.