All land plants encode two isoforms of protoporphyrinogen oxidase (PPO). While PPO1 is predominantly expressed in green tissues and its loss is seedling-lethal in Arabidopsis, the effects of PPO2 deficiency have not been investigated in detail. We identified two ppo2 T-DNA insertion mutants from publicly available collections, one of which (ppo2-2) is a knock-out mutant. While the loss of PPO2 did not result in any obvious phenotype, significant changes in PPO activity were measured in etiolated and root tissues. However, ppo1ppo2 double mutants are embryo-lethal. To shed light on possible functional differences between the two isoforms, PPO2 was overexpressed in the ppo1 background. Although the ppo1 phenotype was partially complemented, even strong overexpression of PPO2 was unable to fully compensate for the loss of PPO1. Analysis of its subcellular localization revealed that PPO2 is found exclusively in chloroplast envelopes, while PPO1 accumulates in thylakoid membranes. A mitochondrial localization of PPO2 in Arabidopsis was ruled out. Since A. thaliana PPO2 does not encode a cleavable transit peptide, integration of the protein into the chloroplast envelope must make use of a non-canonical import route. However, when a chloroplast transit peptide was fused to the N-terminus of PPO2, the enzyme was detected predominantly in thylakoid membranes, and was able to fully complement ppo1. Thus, the two PPO isoforms in Arabidopsis are functionally equivalent, but spatially separated. Their distinctive localizations within plastids thus enable the synthesis of discrete sub-pools of the PPO product protoprophyrin IX, which may serve different cellular needs.