Alpaca fibers have some distinct properties such as softness and warmth, which have not been fully understood in combination with the fiber internal structures. In the present investigation, the internal structures of alpaca fibers have been closely examined under the scanning electron microscope (SEM), especially in the longitudinal direction. The results showed that numerous pigment granules reside loosely inside pockets in brown and dark-brown alpaca fibers. These pigment granules were mainly distributed inside the cortical cells, the medullation regions as well as underneath the cuticles. Their size in the brown alpaca fibers was smaller and more uniformly round than in the dark-brown fibers. These granules in colored alpaca fibers loosen the bundle of cortical cells, providing many crannies in the fibers which may contribute to the superior flexibility, warmth and softness of the fibers. Moreover, there are no heavy metal elements found in the granules. The mordant hydrogen peroxide bleaching employed could eliminate the pigment granules and create many nano-volumes for further dyeing of fibers into more attractive colors.