Interpreting fish remains from sites in the Emigdiano Chumash/southern San Joaquin Valley region is complicated by the diverse set of forces involved in their procurement, use, deposition, and preservation, particularly during the Mission period, when some people from coastal communities made their way to the interior. This paper compares the fish remains from two sites in San Emigdio Canyon with distinct occupational histories (CA-KER-188H and CA-KER-6789). Within these assemblages there is a diachronic shift in the most abundant fish species from Sacramento blackfish (Orthodon microlepidotus) to Sacramento perch (Archoplites interruptus) during the later precolonial and Mission periods. This change is evaluated within this particular cultural and historical context with reference to multiple possible causal factors: taphonomy, environmental change, access to fish or fishing locations, and preference based on taste.