A fundamental question in evolutionary biology concerns the persistence of high levels of genetic variation despite strong stabilizing and directional selection. Here, we perform a fine-scale dissection of selection components using a 25-year genomic, phenotypic, and pedigree dataset in the Federally Threatened Florida Scrub-Jay (Aphelocoma coerulescens). A population of Florida Scrub-Jays at Archbold Biological Station has been studied since 1969, resulting in lifetime fitness measures for thousands of individuals on a 14-generation pedigree. We genotyped every individual in our study population over the past two decades at 15,416 genome-wide SNPs. To test for selection acting on specific life-cycle stages, we modified existing selection component analysis frameworks to take full advantage of exhaustive population sampling. We identified several loci under gametic, viability, or fecundity selection and found evidence of sexual conflict and antagonistic pleiotropy genome-wide. We also estimated indirect genetic effects on different fitness components. Our results provide important insights on the role of selection in maintaining genetic variation in a natural population.