In this article we review some of the main problems encountered by archeobotanical research in Peru as illustrated by studies conducted on two plants (i.e., Solanum tuberorsum L. and Erythroxylum coca Lam.) and briefly describe different archeobotanical analyses in order to understand their contributions, but also their limitations. Moreover, we discuss the development of this discipline in Peru, and retrace some of the main problems encountered. In addition, we present a table containing the first indices of different taxons in Peru. In this table we have purposely presented only data that is accurate in terms of identification and chronological context. Finally, we present a synthesis and a critical evaluation of some of this data.