New and important pennaraptoran specimens continue to be discovered on a regular basis. Yet, with these discoveries the number of viable phylogenetic hypotheses has increased, including ones that challenge the traditional exclusive grouping of dromaeosaurids and troodontids within a monophyletic Deinonychosauria. This chapter section will cover recent efforts to address prevailing phylogenetic uncertainties and controversies, both between and within key clades, including deinonychosaurian monophyly, the phylogenetic position of anchiornithines and scansoriopterygids and the interrelationships of enantiornithines. Whilst recent discoveries mainly from Asia have created much of the latest uncertainties and controversies, brand new material, particularly from Asia, promises to rather fittingly address them. Further curatorship of long-standing phylogenetic datasets and more prevalent use of extended analytical protocols will be essential to meeting this challenge, especially for groups whose boundaries have been blurred. As it becomes increasingly difficult to study all fossil materials owing to their growing numbers and ever disparate locations, broader use of digital fossils and online character databases for character coding is acutely needed to ensure that errors arising from remote rather than first-hand scoring are reduced as far as possible, particularly at this time of rapid data accumulation. Recent taxonomic revisions and newly described taxa also present opportunities to update and revisit clade definitions, e.g., designating neotypes for reference taxa like Troodon formosus.