Scanning electron microscopy has revealed variation in the ultrastructure of distinctive isolated pores in or near the central area of raphid diatoms, with different types of pores being restricted to phylogenetic groups. Thus, the widespread use of the term stigma for all such pores not only hides the structural diversity but also obscures the phylogenetic distribution of the different types. This paper provides images of the different types of isolated pores, particularly refining the discrimination of variants within the Cymbellales, and reveals some interesting ecological patterns. Revised definitions of stigmata and stigmoids are proposed, together with the recognition and definition of another type of stigmoid. The restricted distribution of more precisely defined pore types shows the importance of consistent use of terminology and its relevance to phylogenetic studies.