Some molecular studies supported Genetales as sister to the other seed plants, especially when some chloroplast DNA sequences (all or the third codon positions) were used in phylogenetic reconstruction. This topology was known as the Genetales-sister hypothesis or the Genetales-sister II hypothesis. For clarity, we suggest that it be called “the genetales-other seed plants hypothesis”. Moreover, some studies indicated Genetales as sister to the rest of gymnosperms by analyzing cytoplasmic or nuclear genes. It was referred as the Genetales-sister I hypothesis, and is hereafter called “the genetales-other gymnosperms hypothesis”. This hypothesis was also strongly supported by a couple of recent phylogenomic studies that used combined sequences mostly from expressed sequenced rently, neither the genetales-other seed plants hypothesis nor the genetales-other gymnosperms hypothesis is widely accepted. One of the most important reasons is that the MP method is more easily affected by long branch attraction (LBA) than maximum likelihood. Another reason is that the dayasets used in the phylogenomic analyses contained too many missing data, which might perturb phylogenetic inference. However, while recognizing the shortcomings in data analysis, we should keep in mind that these factors are also problems underlying inference of seed plants, a group experiencing a long evolutionary history and many extinction events.