This second part of the re-investigation of the Eocene Messel palynoflora, using combined light- and scanning electron microscopy (single-grain method), comprises pollen of the Fabales to Caryophyllales. During our study, we discovered one Fabales pollen type, eight Rosales, 20 Fagales, ten Malpighiales, two Myrtales, twelve Sapindales, eleven Malvales, three Santalales, and a single Caryophyllales pollen type. New taxa in the Messel palynoflora includes Erythrina (Fabaceae) and Moraceae. Continuing to compare the palynoflora and meso/macroflora, we notice that additional six families only occur in the microflora, and six other families are represented only by leaf/fruit/seed fossils. Pursuing our assessment of the pros and cons of the combined versus classical quantitative light microscopy studies, we show that the combined method continues to provide a higher diversity of pollen taxa from the plant groups encountered. We report a similar pollen diversity for the orders Fabales to Charyophyllales from a single sample, as previously reported from conventional LM analyses of multi-sampled drill cores. Our combined LM/SEM approach revealed several new floral elements and enabled us to revise several previous botanical affinities based on additional morphological characters observed with SEM.