To determine the taxonomic identities and the systematic positions of some collections of Lindsaea sect. Synaphlebium (Lindsaeaceae) from Papua New Guinea, we conducted morphological comparisons and phylogenetic analyses on the whole section. A total of 22 morphological characters were selected and coded for each of all known taxa in L. sect. Synaphlebium, and were analyzed using maximum parsimony. The datasets containing either of or combined two plastid DNA sequences (trnL-trnF spacer and trnH-psbA spacer) of 37 taxa were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. Morphological comparisons revealed two new species which are formally published here as L. subobscura and L. novoguineensis. Lindsaea subobscura is similar to sympatric L. obscura and L. modesta but differs in the obviously reduced upper pinnules and other characters. Lindsaea novoguineensis is most similar to L. pacifica from Melanesia but differs in having rhomboid pinnules with truncate apices and concave soral receptacles. Molecular analyses resolved L. sect. Synaphlebium and allied species into five well-supported clades, namely L. rigida clade, L. obtusa clade, L. pulchella clade, L. multisora clade, and L. cultrata clade. The new species L. novoguineensis is included in L. obtusa clade; L. subobscura is in L. pulchella clade; whereas the majority of L. sect. Synaphlebium is clustered in L. cultrata clade. As the section Synaphlebium sensu Kramer is strongly suggested as polyphyletic, we propose the concept of a monophyletic L. sect. Synaphlebium in a broad sense that comprises five lineages. The morphological circumscription of L. sect. Synaphlebium sensu lato and the divergence in morphology, habit, and distribution between the five lineages are briefly discussed. Further molecular study is needed to test the systematic positions of 16 other species which are supposed to be within L. sect. Synaphlebium sensu lato but have not been included in this and previous molecular analyses.