The ulvophytes are of particular evolutionary interest because they display a wide morphological and cytological diversity with unique features among green algae. In this review we describe this diversity in an evolutionary perspective, discuss recent progress made towards understanding the genetic underpinning of highly specialized cytomorphological types, such as siphonous cells, and describe the recent progresses made towards the understanding of the peculiar and highly diverse chloroplast genomes found among ulvophytes. We discuss the difficulties in resolving the ancient phylogenetic relationships among ulvophytes, and the core Chlorophyta lineages, even when applying chloroplast phylogenomic analyses. Furthermore, we highlight the advantages and opportunities in using phylotranscriptomics as an alternative tool to resolve difficult phylogenetic relationships and to unveil the evolution of major cyto-morphological innovations and molecular features associated to them.