Pigmentary color is used across nature for signaling, camouflage, and protection. Consequently, the menagerie of colors seen in avian feathers presents an intriguing puzzle for materials engineers, as the same building blocks, pigments and keratin, are used to produce radically different plumage. While the showier coloration mechanism of structural color has been investigated from a materials science perspective, the production of pigmentary color, which may be less constrained, has largely been neglected from a structural perspective. I used Scanning Electron Microscopy (SEM) to image the internal feather structure of twelve species of Southern Capuchino Seedeaters (genus Sporophila) over a range of species, colors, and body feather patches. This group of birds is of particular interest due to its low level of genetic differentiation, which shows divergence mainly in the melanogenesis pathway, and therefore represents an opportunity to study the evolution of the mechanisms of plumage coloration. Key findings include: (1) Fontana Masson stain can be used with backscattered electron SEM to image individual granules of melanin within feathers, (2) white feathers are produced by an absence of melanin, (3) either round or oblong melanosomes can contain primarily eumelanin and produce black or grey feathers while only round melanosomes containing a majority of pheomelanin produce cinnamon or rufous colors, (4) oblong melanosomes are associated with the crown patch, and (5) all oblong melanosomes were found in feathers with at least seven times more eumelanin than pheomelanin. This work contributes to our understanding of the link between plumage differences in the Southern Capuchino Seedeaters and specific genetic changes in the deposition of melanosomes and melanin pigments. Furthermore, it presents a new technique for in situ feather melanin visualization, opening the door for analysis of intra-feather melanin patterning and melanin placement within periodic structural color systems.